MolNFT v1 · #135131 · protein

X-ray structure of the wlarb tdp-quinovose 3,4-ketoisomerase from campylobacter jejuni

5TPU · Putative uncharacterized protein: “X-ray structure of the wlarb tdp-quinovose 3,4-ketoisomerase from campylobacter jejuni”. X-ray diffraction, 2 ligands (TYD, CL), 7 pockets (best druggability 0.70). MolNFT v1 #135131 on GenesisL1…

PDB: 5TPU
Type: protein
Length: 526 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative uncharacterized protein
UniProt: Q9ALS4
Ligands: TYD, CL
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative uncharacterized protein	protein	133	8% helix, 47% strand	Q9ALS4
B	Putative uncharacterized protein	protein	130	7% helix, 48% strand	Q9ALS4
C	Putative uncharacterized protein	protein	131	7% helix, 48% strand	Q9ALS4
D	Putative uncharacterized protein	protein	132	6% helix, 48% strand	Q9ALS4

Ligands and binding sites

TYD · Thymidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 2 copies · chains C, D

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	406	0.70	0.82	81	empty
2	227	0.61	0.81	41	TYD, CL
3	189	0.58	0.81	39	TYD
4	228	0.57	0.79	38	TYD
5	189	0.54	0.78	37	TYD, CL

Interfaces

6 interfaces between chains.

C–D · 1762 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1740 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 525 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 506 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 147 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5TPU · x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni · the same entry in another collection · 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 Q9ALS4
Elsewhere: RCSB PDB 5TPU · PDBe 5TPU · UniProt Q9ALS4

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