9GAL | pdb_00009gal

3-methylbenzoyl-CoA reductase from Thauera chlorobenzoica (subunits MbdON ) + ADP

PDB DOI: https://doi.org/10.2210/pdb9GAL/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: 2.15 Å
R-Value Free:
0.260 (Depositor), 0.258 (DCC)
R-Value Work:
0.238 (Depositor), 0.239 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of 3-methylbenzoyl-CoA reductase

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

To be published.

Macromolecule Content

Total Structure Weight: 616.01 kDa
Atom Count: 42,682
Modeled Residue Count: 5,394
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 5 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 DA [auth G] SDF format, chain MA [auth K] SDF format, chain T [auth C] SDF format, chain XA [auth O] MOL2 format, chain DA [auth G] MOL2 format, chain MA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain XA [auth O] mmCIF format, chain DA [auth G] mmCIF format, chain MA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain XA [auth O]	DA [auth G], MA [auth K], T [auth C], XA [auth O]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain DA [auth G] Focus chain MA [auth K] Focus chain T [auth C] Focus chain XA [auth O] Interactions & Density Focus chain DA [auth G] Focus chain MA [auth K] Focus chain T [auth C] Focus chain XA [auth O]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain BB [auth P] SDF format, chain HA [auth H] SDF format, chain QA [auth L] SDF format, chain X [auth D] MOL2 format, chain BB [auth P] MOL2 format, chain HA [auth H] MOL2 format, chain QA [auth L] MOL2 format, chain X [auth D] mmCIF format, chain BB [auth P] mmCIF format, chain HA [auth H] mmCIF format, chain QA [auth L] mmCIF format, chain X [auth D]	BB [auth P], HA [auth H], QA [auth L], X [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BB [auth P] Focus chain HA [auth H] Focus chain QA [auth L] Focus chain X [auth D] Interactions & Density Focus chain BB [auth P] Focus chain HA [auth H] Focus chain QA [auth L] Focus chain X [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain FA [auth G] SDF format, chain KA [auth J] SDF format, chain PA [auth L] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain TA [auth M] SDF format, chain VA [auth N] SDF format, chain W [auth D] SDF format, chain Z [auth E] SDF format, chain ZA [auth O] SDF format, chain JA [auth I] MOL2 format, chain BA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain KA [auth J] MOL2 format, chain PA [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth M] MOL2 format, chain VA [auth N] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain ZA [auth O] MOL2 format, chain JA [auth I] mmCIF format, chain BA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain KA [auth J] mmCIF format, chain PA [auth L] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth M] mmCIF format, chain VA [auth N] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain ZA [auth O] mmCIF format, chain JA [auth I]	BA [auth F] FA [auth G] JA [auth I] KA [auth J] PA [auth L] BA [auth F], FA [auth G], JA [auth I], KA [auth J], PA [auth L], Q [auth A], R [auth B], TA [auth M], VA [auth N], W [auth D], Z [auth E], ZA [auth O]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain FA [auth G] Focus chain JA [auth I] Focus chain KA [auth J] Focus chain PA [auth L] Focus chain Q [auth A] Focus chain R [auth B] Focus chain TA [auth M] Focus chain VA [auth N] Focus chain W [auth D] Focus chain Z [auth E] Focus chain ZA [auth O] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth G] Focus chain JA [auth I] Focus chain KA [auth J] Focus chain PA [auth L] Focus chain Q [auth A] Focus chain R [auth B] Focus chain TA [auth M] Focus chain VA [auth N] Focus chain W [auth D] Focus chain Z [auth E] Focus chain ZA [auth O]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain AB [auth O] SDF format, chain CA [auth F] SDF format, chain DB [auth P] SDF format, chain GA [auth G] SDF format, chain LA [auth J] SDF format, chain OA [auth K] SDF format, chain S [auth B] SDF format, chain SA [auth L] SDF format, chain UA [auth M] SDF format, chain V [auth C] SDF format, chain WA [auth N] MOL2 format, chain AA [auth E] MOL2 format, chain AB [auth O] MOL2 format, chain CA [auth F] MOL2 format, chain DB [auth P] MOL2 format, chain GA [auth G] MOL2 format, chain LA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth L] MOL2 format, chain UA [auth M] MOL2 format, chain V [auth C] MOL2 format, chain WA [auth N] mmCIF format, chain AA [auth E] mmCIF format, chain AB [auth O] mmCIF format, chain CA [auth F] mmCIF format, chain DB [auth P] mmCIF format, chain GA [auth G] mmCIF format, chain LA [auth J] mmCIF format, chain OA [auth K] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth L] mmCIF format, chain UA [auth M] mmCIF format, chain V [auth C] mmCIF format, chain WA [auth N]	AA [auth E] AB [auth O] CA [auth F] DB [auth P] GA [auth G] AA [auth E], AB [auth O], CA [auth F], DB [auth P], GA [auth G], LA [auth J], OA [auth K], S [auth B], SA [auth L], UA [auth M], V [auth C], WA [auth N]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain AB [auth O] Focus chain CA [auth F] Focus chain DB [auth P] Focus chain GA [auth G] Focus chain LA [auth J] Focus chain OA [auth K] Focus chain S [auth B] Focus chain SA [auth L] Focus chain UA [auth M] Focus chain V [auth C] Focus chain WA [auth N] Interactions & Density Focus chain AA [auth E] Focus chain AB [auth O] Focus chain CA [auth F] Focus chain DB [auth P] Focus chain GA [auth G] Focus chain LA [auth J] Focus chain OA [auth K] Focus chain S [auth B] Focus chain SA [auth L] Focus chain UA [auth M] Focus chain V [auth C] Focus chain WA [auth N]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain CB [auth P] SDF format, chain EA [auth G] SDF format, chain NA [auth K] SDF format, chain RA [auth L] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain YA [auth O] SDF format, chain IA [auth H] MOL2 format, chain CB [auth P] MOL2 format, chain EA [auth G] MOL2 format, chain NA [auth K] MOL2 format, chain RA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth O] MOL2 format, chain IA [auth H] mmCIF format, chain CB [auth P] mmCIF format, chain EA [auth G] mmCIF format, chain NA [auth K] mmCIF format, chain RA [auth L] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth O] mmCIF format, chain IA [auth H]	CB [auth P] EA [auth G] IA [auth H] NA [auth K] RA [auth L] CB [auth P], EA [auth G], IA [auth H], NA [auth K], RA [auth L], U [auth C], Y [auth D], YA [auth O]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CB [auth P] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain NA [auth K] Focus chain RA [auth L] Focus chain U [auth C] Focus chain Y [auth D] Focus chain YA [auth O] Interactions & Density Focus chain CB [auth P] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain NA [auth K] Focus chain RA [auth L] Focus chain U [auth C] Focus chain Y [auth D] Focus chain YA [auth O]