8V4A

Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine

PDB DOI: https://doi.org/10.2210/pdb8V4A/pdb

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

Deposited: 2023-11-28 Released: 2023-12-13
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: 1.96 Å
R-Value Free: 0.224
R-Value Work: 0.177
R-Value Observed: 0.178

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 complexed with L-ethionine

Phillips, R.S.

To be published.

Macromolecule Content

Total Structure Weight: 212.04 kDa
Atom Count: 16,294
Modelled Residue Count: 1,863
Deposited Residue Count: 1,868
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YAR (Subject of Investigation/LOI) Query on YAR Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain M [auth D] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D]	H [auth B], M [auth D]	(2E)-4-(ethylsulfanyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}butanoic acid C₁₄ H₂₁ N₂ O₇ P S BRPPVXUZMWRMGM-YAHQYOFBSA-N		Interactions Focus chain H [auth B] Focus chain M [auth D] Interactions & Density Focus chain H [auth B] Focus chain M [auth D]
YAE (Subject of Investigation/LOI) Query on YAE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C]	F [auth A], K [auth C]	(E)-S-ethyl-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-homocysteine C₁₄ H₂₁ N₂ O₇ P S OMGMVELSRDRWBU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth C]	E [auth A], G [auth A], J [auth C], L [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth C]