MolNFT v1 · #66429 · protein

Bsucp crystal structure

3HQ2 · Bacillus subtilis M32 carboxypeptidase: “Bsucp crystal structure”. X-ray diffraction, 4 ligands (ZN, CL, PO4), 9 pockets (best druggability 0.85). MolNFT v1 #66429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3HQ2
Type: protein
Length: 993 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacillus subtilis M32 carboxypeptidase
EC: 3.4.24.-
UniProt: P50848
Ligands: ZN, CL, PO4, F
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacillus subtilis M32 carboxypeptidase (EC 3.4.24.-)	protein	496	64% helix, 3% strand	P50848
B	Bacillus subtilis M32 carboxypeptidase (EC 3.4.24.-)	protein	497	67% helix, 3% strand	P50848

Ligands and binding sites

ZN · Zinc ion · metal · 7 copies · chains A, B
CL · Chloride ion · ion · 7 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
F · Fluoride ion · ion · chains A, B

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

Pockets

9 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	870	0.85	0.87	110	PO4, ZN, CL
2	743	0.83	0.86	96	PO4, ZN, CL
3	172	0.47	0.76	26	empty
4	135	0.42	0.75	24	empty
5	107	0.41	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 1482 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

3HQ2 · BsuCP Crystal Structure · the same entry in another collection · chain A against A, TM-score 1.00
P50848 · AlphaFold monomer V2.0 prediction for carboxypeptidase 1 (P50848) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P50848
Elsewhere: RCSB PDB 3HQ2 · PDBe 3HQ2 · UniProt P50848

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