9GAI | pdb_00009gai

3-methylbenzoyl-CoA reductase from Thauera chlorobenzoica (MbdONPQ)

PDB DOI: https://doi.org/10.2210/pdb9GAI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thauera chlorobenzoica
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2024-07-29 Released: 2026-02-18
Deposition Author(s): Ermler, U., Boll, M., Demmer, U., Fuchs, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.201 (Depositor), 0.201 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of the methylbenzoyl-CoA reductase

Fuchs, J., Demmer, U., Ermler, U., Boll, M.

To be published.

Macromolecule Content

Total Structure Weight: 616.52 kDa
Atom Count: 45,019
Modeled Residue Count: 5,396
Deposited Residue Count: 5,500
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methylbenzoyl-CoA reductase beta subunit MbdO	A, E, I, M	445	Thauera chlorobenzoica	Mutation(s): 0 Gene Names: Tchl_3426
UniProt
Find proteins for A0A1H5YRX6 (Thauera chlorobenzoica) Explore A0A1H5YRX6 Go to UniProtKB: A0A1H5YRX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1H5YRX6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methylbenzoyl-CoA reductase gamma subunit MbdN	B, F, J, N	388	Thauera chlorobenzoica	Mutation(s): 0 Gene Names: Tchl_3425
UniProt
Find proteins for A0A1H5YT37 (Thauera chlorobenzoica) Explore A0A1H5YT37 Go to UniProtKB: A0A1H5YT37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1H5YT37
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methylbenzoyl-CoA reductase delta subunit MbdP	C, G, K, O	273	Thauera chlorobenzoica	Mutation(s): 0 Gene Names: Tchl_3423
UniProt
Find proteins for A0A1H5YS83 (Thauera chlorobenzoica) Explore A0A1H5YS83 Go to UniProtKB: A0A1H5YS83
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1H5YS83
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methylbenzoyl-CoA reductase alpha subunit MbdQ	D, H, L, P	269	Thauera chlorobenzoica	Mutation(s): 0 Gene Names: Tchl_3424
UniProt
Find proteins for A0A1H5YSL0 (Thauera chlorobenzoica) Explore A0A1H5YSL0 Go to UniProtKB: A0A1H5YSL0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1H5YSL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain CB [auth K] SDF format, chain NA [auth G] SDF format, chain RB [auth O] SDF format, chain Z [auth C] MOL2 format, chain CB [auth K] MOL2 format, chain NA [auth G] MOL2 format, chain RB [auth O] MOL2 format, chain Z [auth C] mmCIF format, chain CB [auth K] mmCIF format, chain NA [auth G] mmCIF format, chain RB [auth O] mmCIF format, chain Z [auth C]	CB [auth K], NA [auth G], RB [auth O], Z [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain CB [auth K] Focus chain NA [auth G] Focus chain RB [auth O] Focus chain Z [auth C] Interactions & Density Focus chain CB [auth K] Focus chain NA [auth G] Focus chain RB [auth O] Focus chain Z [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain FB [auth L] SDF format, chain QA [auth H] SDF format, chain VB [auth P] MOL2 format, chain CA [auth D] MOL2 format, chain FB [auth L] MOL2 format, chain QA [auth H] MOL2 format, chain VB [auth P] mmCIF format, chain CA [auth D] mmCIF format, chain FB [auth L] mmCIF format, chain QA [auth H] mmCIF format, chain VB [auth P]	CA [auth D], FB [auth L], QA [auth H], VB [auth P]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth D] Focus chain FB [auth L] Focus chain QA [auth H] Focus chain VB [auth P] Interactions & Density Focus chain CA [auth D] Focus chain FB [auth L] Focus chain QA [auth H] Focus chain VB [auth P]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain EA [auth E] SDF format, chain EB [auth K] SDF format, chain IB [auth M] SDF format, chain JA [auth F] SDF format, chain NB [auth N] SDF format, chain PA [auth G] SDF format, chain Q [auth A] SDF format, chain TA [auth I] SDF format, chain TB [auth O] SDF format, chain W [auth B] SDF format, chain XA [auth J] MOL2 format, chain BA [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth K] MOL2 format, chain IB [auth M] MOL2 format, chain JA [auth F] MOL2 format, chain NB [auth N] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth I] MOL2 format, chain TB [auth O] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth J] mmCIF format, chain BA [auth C] mmCIF format, chain EA [auth E] mmCIF format, chain EB [auth K] mmCIF format, chain IB [auth M] mmCIF format, chain JA [auth F] mmCIF format, chain NB [auth N] mmCIF format, chain PA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain TA [auth I] mmCIF format, chain TB [auth O] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth J]	BA [auth C] EA [auth E] EB [auth K] IB [auth M] JA [auth F] BA [auth C], EA [auth E], EB [auth K], IB [auth M], JA [auth F], NB [auth N], PA [auth G], Q [auth A], TA [auth I], TB [auth O], W [auth B], XA [auth J]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain EA [auth E] Focus chain EB [auth K] Focus chain IB [auth M] Focus chain JA [auth F] Focus chain NB [auth N] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain TA [auth I] Focus chain TB [auth O] Focus chain W [auth B] Focus chain XA [auth J] Interactions & Density Focus chain BA [auth C] Focus chain EA [auth E] Focus chain EB [auth K] Focus chain IB [auth M] Focus chain JA [auth F] Focus chain NB [auth N] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain TA [auth I] Focus chain TB [auth O] Focus chain W [auth B] Focus chain XA [auth J]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain LB [auth M] SDF format, chain MB [auth M] SDF format, chain PB [auth N] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain VA [auth I] SDF format, chain WA [auth I] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain LB [auth M] MOL2 format, chain MB [auth M] MOL2 format, chain PB [auth N] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth I] MOL2 format, chain WA [auth I] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain LB [auth M] mmCIF format, chain MB [auth M] mmCIF format, chain PB [auth N] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth I] mmCIF format, chain WA [auth I]	HA [auth E] IA [auth E] LB [auth M] MB [auth M] PB [auth N] HA [auth E], IA [auth E], LB [auth M], MB [auth M], PB [auth N], S [auth A], T [auth A], U [auth A], VA [auth I], WA [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Focus chain IA [auth E] Focus chain LB [auth M] Focus chain MB [auth M] Focus chain PB [auth N] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain VA [auth I] Focus chain WA [auth I] Interactions & Density Focus chain HA [auth E] Focus chain IA [auth E] Focus chain LB [auth M] Focus chain MB [auth M] Focus chain PB [auth N] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain VA [auth I] Focus chain WA [auth I]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AB [auth J] SDF format, chain BB [auth J] SDF format, chain MA [auth F] SDF format, chain QB [auth N] SDF format, chain UB [auth O] SDF format, chain V [auth A] SDF format, chain XB [auth P] SDF format, chain Y [auth B] SDF format, chain ZA [auth J] MOL2 format, chain AB [auth J] MOL2 format, chain BB [auth J] MOL2 format, chain MA [auth F] MOL2 format, chain QB [auth N] MOL2 format, chain UB [auth O] MOL2 format, chain V [auth A] MOL2 format, chain XB [auth P] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth J] mmCIF format, chain AB [auth J] mmCIF format, chain BB [auth J] mmCIF format, chain MA [auth F] mmCIF format, chain QB [auth N] mmCIF format, chain UB [auth O] mmCIF format, chain V [auth A] mmCIF format, chain XB [auth P] mmCIF format, chain Y [auth B] mmCIF format, chain ZA [auth J]	AB [auth J] BB [auth J] MA [auth F] QB [auth N] UB [auth O] AB [auth J], BB [auth J], MA [auth F], QB [auth N], UB [auth O], V [auth A], XB [auth P], Y [auth B], ZA [auth J]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain BB [auth J] Focus chain MA [auth F] Focus chain QB [auth N] Focus chain UB [auth O] Focus chain V [auth A] Focus chain XB [auth P] Focus chain Y [auth B] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth J] Focus chain BB [auth J] Focus chain MA [auth F] Focus chain QB [auth N] Focus chain UB [auth O] Focus chain V [auth A] Focus chain XB [auth P] Focus chain Y [auth B] Focus chain ZA [auth J]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain KB [auth M] SDF format, chain LA [auth F] SDF format, chain R [auth A] SDF format, chain UA [auth I] SDF format, chain YA [auth J] MOL2 format, chain GA [auth E] MOL2 format, chain KB [auth M] MOL2 format, chain LA [auth F] MOL2 format, chain R [auth A] MOL2 format, chain UA [auth I] MOL2 format, chain YA [auth J] mmCIF format, chain GA [auth E] mmCIF format, chain KB [auth M] mmCIF format, chain LA [auth F] mmCIF format, chain R [auth A] mmCIF format, chain UA [auth I] mmCIF format, chain YA [auth J]	GA [auth E] KB [auth M] LA [auth F] R [auth A] UA [auth I] GA [auth E], KB [auth M], LA [auth F], R [auth A], UA [auth I], YA [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth E] Focus chain KB [auth M] Focus chain LA [auth F] Focus chain R [auth A] Focus chain UA [auth I] Focus chain YA [auth J] Interactions & Density Focus chain GA [auth E] Focus chain KB [auth M] Focus chain LA [auth F] Focus chain R [auth A] Focus chain UA [auth I] Focus chain YA [auth J]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DA [auth D] SDF format, chain DB [auth K] SDF format, chain FA [auth E] SDF format, chain GB [auth L] SDF format, chain HB [auth L] SDF format, chain JB [auth M] SDF format, chain KA [auth F] SDF format, chain OA [auth G] SDF format, chain OB [auth N] SDF format, chain RA [auth H] SDF format, chain SA [auth H] SDF format, chain SB [auth O] SDF format, chain WB [auth P] SDF format, chain X [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth K] MOL2 format, chain FA [auth E] MOL2 format, chain GB [auth L] MOL2 format, chain HB [auth L] MOL2 format, chain JB [auth M] MOL2 format, chain KA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain OB [auth N] MOL2 format, chain RA [auth H] MOL2 format, chain SA [auth H] MOL2 format, chain SB [auth O] MOL2 format, chain WB [auth P] MOL2 format, chain X [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth K] mmCIF format, chain FA [auth E] mmCIF format, chain GB [auth L] mmCIF format, chain HB [auth L] mmCIF format, chain JB [auth M] mmCIF format, chain KA [auth F] mmCIF format, chain OA [auth G] mmCIF format, chain OB [auth N] mmCIF format, chain RA [auth H] mmCIF format, chain SA [auth H] mmCIF format, chain SB [auth O] mmCIF format, chain WB [auth P] mmCIF format, chain X [auth B]	AA [auth C] DA [auth D] DB [auth K] FA [auth E] GB [auth L] AA [auth C], DA [auth D], DB [auth K], FA [auth E], GB [auth L], HB [auth L], JB [auth M], KA [auth F], OA [auth G], OB [auth N], RA [auth H], SA [auth H], SB [auth O], WB [auth P], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain DA [auth D] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain GB [auth L] Focus chain HB [auth L] Focus chain JB [auth M] Focus chain KA [auth F] Focus chain OA [auth G] Focus chain OB [auth N] Focus chain RA [auth H] Focus chain SA [auth H] Focus chain SB [auth O] Focus chain WB [auth P] Focus chain X [auth B] Interactions & Density Focus chain AA [auth C] Focus chain DA [auth D] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain GB [auth L] Focus chain HB [auth L] Focus chain JB [auth M] Focus chain KA [auth F] Focus chain OA [auth G] Focus chain OB [auth N] Focus chain RA [auth H] Focus chain SA [auth H] Focus chain SB [auth O] Focus chain WB [auth P] Focus chain X [auth B]