MolNFT v1 · #117027 · protein

Holo trpb from pyrococcus furiosus

5DVZ · Tryptophan synthase beta chain 1: “Holo trpb from pyrococcus furiosus”. X-ray diffraction, 2 ligands (NA, PO4), 14 pockets (best druggability 0.83). MolNFT v1 #117027 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DVZ
Type: protein
Length: 1,535 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tryptophan synthase beta chain 1
EC: 4.2.1.20
UniProt: Q8U093
Ligands: NA, PO4
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tryptophan synthase beta chain 1 (EC 4.2.1.20)	protein	384	48% helix, 20% strand	Q8U093
B	Tryptophan synthase beta chain 1 (EC 4.2.1.20)	protein	382	49% helix, 20% strand	Q8U093
C	Tryptophan synthase beta chain 1 (EC 4.2.1.20)	protein	384	49% helix, 20% strand	Q8U093
D	Tryptophan synthase beta chain 1 (EC 4.2.1.20)	protein	385	48% helix, 20% strand	Q8U093

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	229	0.83	0.96	50	empty
2	936	0.80	0.82	102	empty
3	127	0.79	0.97	21	PO4
4	105	0.78	0.98	21	PO4
5	138	0.78	0.96	39	empty

Interfaces

4 interfaces between chains.

C–D · 1858 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1812 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 226 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 181 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (cofactor).

Compared structures

5DVZ · Holo TrpB from Pyrococcus furiosus · the same entry in another collection · chain D against D, TM-score 1.00
Q8U093 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain 1 (Q8U093) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q8U093
Elsewhere: RCSB PDB 5DVZ · PDBe 5DVZ · UniProt Q8U093

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