MolNFT v1 · #93315 · protein

Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate

4GYS: “Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate”. X-ray diffraction, 7 pockets (best druggability 0.75). MolNFT v1 #93315 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GYS
Type: protein
Length: 921 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Allophanate hydrolase
EC: 3.5.1.54
UniProt: Q0BRB0
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Allophanate hydrolase (EC 3.5.1.54)	protein	460	39% helix, 18% strand	Q0BRB0
B	Allophanate hydrolase (EC 3.5.1.54)	protein	461	40% helix, 18% strand	Q0BRB0

Ligands and binding sites

MLI · Malonate ion · additive · 4 copies · chains A, B

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

Pockets

7 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	1064	0.75	0.77	76	empty
2	52	0.52	0.87	15	empty
3	54	0.49	0.85	13	empty
4	103	0.46	0.80	31	MLI
5	70	0.38	0.79	15	empty

Interfaces

1 interface between chains.

A–B · 1168 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4GYS · Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate · 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 Q0BRB0
Elsewhere: RCSB PDB 4GYS · PDBe 4GYS · UniProt Q0BRB0

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