MolNFT v1 · #122058 · protein

Crystal structure of a plant enzyme

5IE0 · Oxalate--CoA ligase: “Crystal structure of a plant enzyme”. X-ray diffraction, 1 ligand (SRT), 11 pockets (best druggability 0.83). MolNFT v1 #122058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IE0
Type: protein
Length: 1,006 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxalate--CoA ligase
EC: 6.2.1.8
UniProt: Q9SMT7
Ligands: SRT
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Oxalate--CoA ligase (EC 6.2.1.8)	protein	503	33% helix, 26% strand	Q9SMT7

Ligands and binding sites

SRT · S,R meso-tartaric acid · ligand · 4 copies · chains A, B

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

Pockets

11 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	945	0.83	0.84	82	SRT
2	1097	0.82	0.83	93	SRT
3	547	0.70	0.79	76	SRT
4	57	0.60	0.91	17	empty
5	246	0.56	0.78	51	empty

Interfaces

1 interface between chains.

A–B · 796 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5IE0 · Crystal structure of a plant enzyme · the same entry in another collection · chain A against A, TM-score 1.00
Q9SMT7 · AlphaFold monomer V2.0 prediction for oxalate--CoA ligase (Q9SMT7) · 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 Q9SMT7
Elsewhere: RCSB PDB 5IE0 · PDBe 5IE0 · UniProt Q9SMT7

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