9BNJ

Proteus vulgaris tryptophan indole-lyase aminoacrylate complex with benzimidazole

PDB DOI: https://doi.org/10.2210/pdb9BNJ/pdb

Classification: LYASE
Organism(s): Proteus vulgaris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-02 Released: 2024-05-29
Deposition Author(s): Phillips, R.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.180
R-Value Work: 0.158
R-Value Observed: 0.159

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

Proteus vulgaris tryptophan indole-lyase aminoacrylate complex with benzimidazole

Phillips, R.S.

To be published.

Macromolecule Content

Total Structure Weight: 212.36 kDa
Atom Count: 18,923
Modelled Residue Count: 1,854
Deposited Residue Count: 1,868
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanase	A, B, C, D	467	Proteus vulgaris	Mutation(s): 0 Gene Names: tnaA EC: 4.1.99.1
UniProt
Find proteins for P28796 (Proteus vulgaris) Explore P28796 Go to UniProtKB: P28796
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28796
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0JO (Subject of Investigation/LOI) Query on 0JO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D]	H [auth A], M [auth B], P [auth C], S [auth D]	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid C₁₁ H₁₃ N₂ O₇ P BHIGINKEEFZJGX-YIXHJXPBSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D]
BZI (Subject of Investigation/LOI) Query on BZI Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D]	F [auth A], I [auth A], L [auth B], O [auth C], R [auth D]	BENZIMIDAZOLE C₇ H₆ N₂ HYZJCKYKOHLVJF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth A] SDF format, chain N [auth C] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth C]	E [auth A], J [auth A], N [auth C], Q [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain Q [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]