MolNFT v1 · #38516 · protein

Structure of the yeast nicotinamidase PNC1P

2H0R: “Structure of the yeast nicotinamidase PNC1P”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.73). MolNFT v1 #38516 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2H0R
Type: protein
Length: 1,512 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nicotinamidase
EC: 3.5.1.19
UniProt: P53184
Ligands: ZN
Pockets: 16 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Nicotinamidase (EC 3.5.1.19)	protein	216	31% helix, 26% strand	P53184

Ligands and binding sites

ZN · Zinc ion · metal · 7 copies · chains A, B, C, D, E, F, G

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

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	692	0.73	0.79	49	empty
2	709	0.72	0.79	46	empty
3	694	0.72	0.79	46	empty
4	680	0.71	0.78	52	empty
5	641	0.71	0.78	45	empty

Interfaces

7 interfaces between chains.

D–E · 641 Å² buried · 8 hydrogen bonds · protein-protein
F–G · 632 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 630 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 624 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 609 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2H0R · Structure of the Yeast Nicotinamidase Pnc1p · the same entry in another collection · chain G against G, TM-score 1.00
P53184 · AlphaFold monomer V2.0 prediction for nicotinamidase (P53184) · 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 P53184
Elsewhere: RCSB PDB 2H0R · PDBe 2H0R · UniProt P53184

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