MolNFT v1 · #51434 · protein

Crystal structure of an engineered urocanase tetramer

2V7G · Urocanate hydratase: “Crystal structure of an engineered urocanase tetramer”. X-ray diffraction, 1 ligand (NAD), 16 pockets (best druggability 0.79). MolNFT v1 #51434 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2V7G
Type: protein
Length: 2,212 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urocanate hydratase
EC: 4.2.1.49
UniProt: P25080
Ligands: NAD
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Urocanate hydratase (EC 4.2.1.49)	protein	553	45% helix, 15% strand	P25080

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 9 copies · chains A, B, D
ACT · Acetate ion · additive · 7 copies · chains A, B, D, C

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

Pockets

16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	805	0.79	0.82	88	ACT, NAD
2	476	0.79	0.86	66	ACT, NAD
3	489	0.79	0.86	65	ACT, NAD
4	753	0.78	0.82	83	NAD
5	679	0.70	0.77	66	GOL

Interfaces

4 interfaces between chains.

B–D · 3272 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 3202 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 300 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 283 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2V7G · Crystal Structure of an Engineered Urocanase Tetramer · the same entry in another collection · chain A against A, TM-score 1.00
P25080 · AlphaFold monomer V2.0 prediction for urocanate hydratase (P25080) · a predicted model of the same protein · 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 P25080
Elsewhere: RCSB PDB 2V7G · PDBe 2V7G · UniProt P25080

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