MolNFT v1 · #123478 · protein

Crystal structure of ribose-5-phosphate isomerase from brucella melitensis 16M

5JLA · Putative short-chain DEHYDROGENASE/REDUCTASE: “Crystal structure of ribose-5-phosphate isomerase from brucella melitensis 16M”. X-ray diffraction, 1 ligand (NAD), 14 pockets (best druggability 0.83). MolNFT v1 #123478 on GenesisL1…

PDB: 5JLA
Type: protein
Length: 1,032 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative short-chain DEHYDROGENASE/REDUCTASE
UniProt: Q13GR0
Ligands: NAD
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	257	50% helix, 17% strand	Q13GR0
B, C	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	258	50% helix, 17% strand	Q13GR0
D	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	259	50% helix, 17% strand	Q13GR0

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.83	0.84	65	empty
2	427	0.77	0.86	48	NAD
3	416	0.76	0.85	48	NAD
4	416	0.76	0.85	48	NAD
5	395	0.75	0.85	44	NAD

Interfaces

6 interfaces between chains.

A–B · 1614 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1607 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1373 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1361 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1057 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5JLA · Crystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M · the same entry in another collection · chain B against B, 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 Q13GR0
Elsewhere: RCSB PDB 5JLA · PDBe 5JLA · UniProt Q13GR0

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