MolNFT v1 · #137852 · protein

Tryptophan indole-lyase

5W1B · Tryptophanase: “Tryptophan indole-lyase”. X-ray diffraction, 1 ligand (K), 20 pockets (best druggability 0.77). MolNFT v1 #137852 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5W1B
Type: protein
Length: 1,864 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tryptophanase
EC: 4.1.99.1
UniProt: P28796
Ligands: K
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Tryptophanase (EC 4.1.99.1)	protein	466	44% helix, 16% strand	P28796

Ligands and binding sites

K · Potassium ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	841	0.77	0.80	78	empty
2	830	0.77	0.80	74	empty
3	735	0.76	0.81	66	empty
4	786	0.75	0.79	61	empty
5	80	0.73	0.97	25	empty

Interfaces

6 interfaces between chains.

A–B · 2268 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2231 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 1818 Å² buried · 41 hydrogen bonds · protein-protein
A–C · 1717 Å² buried · 40 hydrogen bonds · protein-protein
A–D · 391 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (cofactor).

Compared structures

5W1B · Tryptophan indole-lyase · the same entry in another collection · chain A against A, TM-score 1.00
P28796 · AlphaFold monomer V2.0 prediction for tryptophanase (P28796) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P28796
Elsewhere: RCSB PDB 5W1B · PDBe 5W1B · UniProt P28796

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