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E.COLI methionine aminopeptidase transition-state inhibitor complex

Analyse E.COLI methionine aminopeptidase transition-state inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MAT
Type: protein
Length: 267 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: Methionine aminopeptidase; bestatin-based inhibitor…
EC: 3.4.11.18
UniProt: P07906
Ligands: CO, NA
Pockets: 1 · best druggability 0.25

Structure

x-ray diffraction · resolution 2 · 2 distinct chains · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionine aminopeptidase (EC 3.4.11.18)	protein	264	29% helix, 27% strand	P07906
I	bestatin-based inhibitor (3R)-amino-(2S)-hydroxyheptanoyl-l-Ala-l-Leu-l-Val-l-Phe-OMe	protein	3	0% helix, 0% strand	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · 2 copies · chains A, I
NA · Sodium ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.25	0.73	13	empty

Interfaces

1 interface between chains.

A–I · 365 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

3MAT · E.COLI methionine aminopeptidase transition-state inhibitor complex · the same entry in another collection · 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 P07906
Elsewhere: RCSB PDB 3MAT · PDBe 3MAT · UniProt P07906

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