9TPF | pdb_00009tpf

The structure of the orthorhombic crystal form of the type II ribosome inactivating protein from Winter Aconite Eranthis hyemalis.

PDB DOI: https://doi.org/10.2210/pdb9TPF/pdb

Classification: TOXIN
Organism(s): Eranthis hyemalis
Mutation(s): No

Deposited: 2025-12-18 Released: 2026-01-21
Deposition Author(s): Cooper, J.B., Palmer, R.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.233 (Depositor), 0.247 (DCC)
R-Value Work:
0.182 (Depositor), 0.192 (DCC)

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

The Structure of the Type II Ribosome Inactivating Protein from Winter Aconite Eranthis hyemalis.

McConnell, M.-T., Talbert, R.C., Lee, J.C., Lisgarten, D.R., Lisgarten, J., Bertolo, E., Harvey, S.C., Levy, C.W., Lowe, E.D., Cooper, J.B., Naylor, C., Quiroz, R., Borges, R., Prince, S.M., Palmer, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 57.76 kDa
Atom Count: 4,739
Modeled Residue Count: 502
Deposited Residue Count: 503
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosidase	A	241	Eranthis hyemalis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	B	262	Eranthis hyemalis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A], D [auth A], L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	J [auth B], K [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
AH2 Query on AH2 Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	1-deoxy-alpha-D-mannopyranose C₆ H₁₂ O₅ MPCAJMNYNOGXPB-KVTDHHQDSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B]	G [auth A], I [auth A], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]