MolNFT v1 · #14246 · protein

Aminopeptidase P from escherichia COLI

1M35: “Aminopeptidase P from escherichia COLI”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.86). MolNFT v1 #14246 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1M35
Type: protein
Length: 2,640 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminopeptidase P
EC: 3.4.11.9
UniProt: P15034
Ligands: MN
Pockets: 20 · best druggability 0.86

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Aminopeptidase P (EC 3.4.11.9)	protein	440	41% helix, 19% strand	P15034

Ligands and binding sites

MN · Manganese (II) ion · metal · 12 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	923	0.86	0.88	96	MN
2	306	0.83	0.94	43	empty
3	1190	0.82	0.83	107	MN
4	1156	0.81	0.83	113	MN
5	1036	0.81	0.83	103	empty

Interfaces

7 interfaces between chains.

A–D · 2207 Å² buried · 45 hydrogen bonds · protein-protein
B–C · 2203 Å² buried · 48 hydrogen bonds · protein-protein
C–D · 687 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 684 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 662 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1M35 · Aminopeptidase P from Escherichia coli · the same entry in another collection · chain F against F, TM-score 1.00
P15034 · AlphaFold monomer V2.0 prediction for xaa-pro aminopeptidase (P15034) · 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 P15034
Elsewhere: RCSB PDB 1M35 · PDBe 1M35 · UniProt P15034

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