MolNFT v1 · #65828 · protein

High pH native structure of leucine aminopeptidase from pseudomonas putida

3H8F · Cytosol aminopeptidase: “High pH native structure of leucine aminopeptidase from pseudomonas putida”. X-ray diffraction, 4 ligands (BCT, ZN, MN), 20 pockets (best druggability 0.73). MolNFT v1 #65828 on GenesisL1: 3D structure…

PDB: 3H8F
Type: protein
Length: 2,982 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytosol aminopeptidase
EC: 3.4.11.1
UniProt: O86436
Ligands: BCT, ZN, MN, K
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Cytosol aminopeptidase (EC 3.4.11.1)	protein	497	38% helix, 21% strand	O86436

Ligands and binding sites

BCT · Bicarbonate ion · ligand · 6 copies · chains A, B, C, D, E, F
ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	962	0.73	0.76	100	BCT
2	921	0.72	0.77	78	empty
3	957	0.72	0.76	85	BCT
4	588	0.68	0.78	45	empty
5	594	0.67	0.77	46	empty

Interfaces

12 interfaces between chains.

B–F · 1251 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1244 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1178 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1019 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 993 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3H8F · High pH native structure of leucine aminopeptidase from Pseudomonas putida · the same entry in another collection · chain F against F, TM-score 1.00
O86436 · AlphaFold monomer V2.0 prediction for cytosol aminopeptidase (O86436) · 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 O86436
Elsewhere: RCSB PDB 3H8F · PDBe 3H8F · UniProt O86436

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