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Crystal structure of a plant enzyme

Analyse Crystal structure of a plant enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IE2
Type: protein
Length: 1,012 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: ATP, MG
Pockets: 16 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Oxalate--CoA ligase (EC 6.2.1.8)	protein	506	33% helix, 27% strand	Q9SMT7

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
ACY · Acetic acid · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	617	0.82	0.87	76	ATP, MG, ACY
2	640	0.81	0.86	75	ATP, MG, ACY
3	512	0.68	0.79	78	empty
4	174	0.63	0.84	25	empty
5	155	0.61	0.84	22	empty

Interfaces

1 interface between chains.

A–B · 820 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5IE2 · 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 A 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 5IE2 · PDBe 5IE2 · UniProt Q9SMT7

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