MolNFT v1 · #137850 · protein

Tryptophan indole-lyase complex with oxindolyl-L-alanine

5W19 · Tryptophanase: “Tryptophan indole-lyase complex with oxindolyl-L-alanine”. X-ray diffraction, 2 ligands (9TD, K), 20 pockets (best druggability 0.81). MolNFT v1 #137850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5W19
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: 9TD, K
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Tryptophanase (EC 4.1.99.1)	protein	466	45% helix, 16% strand	P28796

Ligands and binding sites

9TD · 1-carboxy-1-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]azaniumyl}-2-[(3R)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-ide · ligand · 4 copies · chains A, B, C, D
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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	140	0.81	0.98	35	9TD
2	149	0.81	0.97	34	9TD
3	159	0.81	0.97	35	9TD
4	133	0.80	0.98	35	9TD
5	54	0.73	0.98	13	empty

Interfaces

6 interfaces between chains.

C–D · 2339 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2317 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 1750 Å² buried · 40 hydrogen bonds · protein-protein
B–D · 1728 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 387 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5W19 · Tryptophan indole-lyase complex with oxindolyl-L-alanine · the same entry in another collection · chain C against C, 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 0.98

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 5W19 · PDBe 5W19 · UniProt P28796

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