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Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from thermotoga maritima

Analyse Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AX6
Type: protein
Length: 1,438 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
UniProt: Q9WYS8
Ligands: ADP
Pockets: 13 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphoribosylaminoimidazole carboxylase, ATPase subunit	protein	360	32% helix, 31% strand	Q9WYS8
C	Phosphoribosylaminoimidazole carboxylase, ATPase subunit	protein	359	32% helix, 30% strand	Q9WYS8
D	Phosphoribosylaminoimidazole carboxylase, ATPase subunit	protein	359	32% helix, 30% strand	Q9WYS8

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	971	0.86	0.87	120	empty
2	899	0.83	0.85	91	empty
3	216	0.48	0.75	36	ADP
4	156	0.45	0.75	22	empty
5	182	0.44	0.74	26	empty

Interfaces

4 interfaces between chains.

C–D · 1584 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1520 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 452 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 143 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 modified (engineered).

Compared structures

3AX6 · Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from Thermotoga… · 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
Every structure of UniProt Q9WYS8
Elsewhere: RCSB PDB 3AX6 · PDBe 3AX6 · UniProt Q9WYS8

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