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Ca-substituted form of E. COLI aminopeptidase P

Analyse Ca-substituted form of E. COLI aminopeptidase P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1W2M
Type: protein
Length: 2,634 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xaa-pro aminopeptidase
EC: 3.4.11.9
UniProt: P15034
Ligands: CA, CL
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Xaa-pro aminopeptidase (EC 3.4.11.9)	protein	439	41% helix, 19% strand	P15034
B	Xaa-pro aminopeptidase (EC 3.4.11.9)	protein	437	41% helix, 19% strand	P15034
D, F	Xaa-pro aminopeptidase (EC 3.4.11.9)	protein	440	41% helix, 19% strand	P15034

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
IPA · Isopropyl alcohol · additive · 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.86	0.87	124	empty
2	276	0.82	0.94	40	empty
3	1128	0.81	0.83	100	CA
4	1141	0.81	0.82	124	empty
5	946	0.81	0.83	100	empty

Interfaces

8 interfaces between chains.

B–C · 2258 Å² buried · 50 hydrogen bonds · protein-protein
A–D · 2252 Å² buried · 47 hydrogen bonds · protein-protein
E–F · 722 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 706 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 701 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (oxidation).

Compared structures

1W2M · Ca-substituted form of E. coli aminopeptidase P · 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 1W2M · PDBe 1W2M · UniProt P15034

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