MolNFT v1 · #153044 · protein

Crystal structure of ribose-5-phosphate isomerase a from ochrobactrum sp. CSL1

6J1K: “Crystal structure of ribose-5-phosphate isomerase a from ochrobactrum sp. CSL1”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #153044 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6J1K
Type: protein
Length: 456 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribose-5-phosphate isomerase a
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribose-5-phosphate isomerase a	protein	230	31% helix, 24% strand	—
B	Ribose-5-phosphate isomerase a	protein	226	30% helix, 29% strand	—

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	432	0.63	0.77	64	empty
2	57	0.38	0.80	25	empty
3	55	0.38	0.81	20	PEG
4	51	0.35	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 1169 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6J1K · Crystal structure of ribose-5-phosphate isomerase A from Ochrobactrum sp. CSL1 · 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
Elsewhere: RCSB PDB 6J1K · PDBe 6J1K

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