Research workbench

Saicar synthetase (type-1) in complex with gmp

Analyse Saicar synthetase (type-1) in complex with gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4O84
Type: protein
Length: 454 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoribosylaminoimidazole-succinocarboxamide synthase
EC: 6.3.2.6
UniProt: O57978
Ligands: 5GP, CD, PO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6)	protein	227	30% helix, 33% strand	O57978

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
CD · Cadmium ion · metal · 14 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
BU1 · 1,4-butanediol · additive · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	670	0.72	0.79	60	CD
2	468	0.63	0.77	33	CD, 5GP, PO4
3	424	0.60	0.76	31	CD, 5GP, PO4

Interfaces

1 interface between chains.

A–B · 310 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

4O84 · SAICAR synthetase (Type-1) in complex with GMP · the same entry in another collection · chain A against A, TM-score 1.00
O57978 · AlphaFold monomer V2.0 prediction for phosphoribosylaminoimidazole- succinocarboxamide… · 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 O57978
Elsewhere: RCSB PDB 4O84 · PDBe 4O84 · UniProt O57978

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