MolNFT v1 · #12215 · protein

Structure of pyrococcus furiosus carboxypeptidase nat-pb

1KA4 · M32 carboxypeptidase: “Structure of pyrococcus furiosus carboxypeptidase nat-pb”. X-ray diffraction, 1 ligand (PB), 4 pockets (best druggability 0.78). MolNFT v1 #12215 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KA4
Type: protein
Length: 497 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: M32 carboxypeptidase
UniProt: Q8U3L0
Ligands: PB
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	M32 carboxypeptidase	protein	497	69% helix, 4% strand	Q8U3L0

Ligands and binding sites

PB · Lead (II) ion · metal · chains A

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

Pockets

4 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	1036	0.78	0.80	87	empty
2	91	0.60	0.87	17	empty
3	143	0.54	0.80	20	empty
4	71	0.39	0.79	13	empty

Compared structures

1KA4 · Structure of Pyrococcus furiosus carboxypeptidase Nat-Pb · the same entry in another collection · chain A against A, TM-score 1.00
Q8U3L0 · AlphaFold monomer V2.0 prediction for thermostable carboxypeptidase 1 (Q8U3L0) · 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 Q8U3L0
Elsewhere: RCSB PDB 1KA4 · PDBe 1KA4 · UniProt Q8U3L0

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