MolNFT v1 · #35234 · protein

Crystal structure of human nmprtase complexed with nicotinamide

2E5D · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nmprtase complexed with nicotinamide”. X-ray diffraction, 1 ligand (NCA), 5 pockets (best druggability 0.79). MolNFT v1 #35234 on GenesisL1: 3D structure, binding…

PDB: 2E5D
Type: protein
Length: 932 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nicotinamide phosphoribosyltransferase
EC: 2.4.2.12
UniProt: P43490
Ligands: NCA
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nicotinamide phosphoribosyltransferase (EC 2.4.2.12)	protein	466	41% helix, 19% strand	P43490

Ligands and binding sites

NCA · Nicotinamide · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	680	0.79	0.84	80	NCA
2	690	0.78	0.83	82	NCA
3	700	0.74	0.80	62	empty
4	52	0.32	0.78	14	empty
5	50	0.29	0.76	11	empty

Interfaces

1 interface between chains.

A–B · 4320 Å² buried · 79 hydrogen bonds · protein-protein

Compared structures

2E5D · Crystal structure of Human NMPRTase complexed with nicotinamide · 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 P43490
Elsewhere: RCSB PDB 2E5D · PDBe 2E5D · UniProt P43490

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