MolNFT v1 · #27053 · protein

2.4A X-ray structure of urocanase protein complexed with NAD

1X87: “2.4A X-ray structure of urocanase protein complexed with NAD”. X-ray diffraction, 1 ligand (NAD), 5 pockets (best druggability 0.77). MolNFT v1 #27053 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1X87
Type: protein
Length: 988 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urocanase protein
EC: 4.2.1.49
Ligands: NAD
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Urocanase protein (EC 4.2.1.49)	protein	495	47% helix, 18% strand	—
B	Urocanase protein (EC 4.2.1.49)	protein	493	47% helix, 17% strand	—

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

5 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	982	0.77	0.79	99	NAD
2	698	0.75	0.80	75	NAD
3	83	0.35	0.76	17	empty
4	100	0.35	0.74	24	empty
5	55	0.27	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 2616 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 modified (engineered).

Compared structures

1X87 · 2.4A X-ray structure of Urocanase protein complexed with NAD · 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
Elsewhere: RCSB PDB 1X87 · PDBe 1X87

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