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Vibrio cholerae methionine aminopeptidase in holo form

Analyse Vibrio cholerae methionine aminopeptidase in holo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KSG
Type: protein
Length: 558 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine aminopeptidase
EC: 3.4.11.18
UniProt: Q9KPV1
Ligands: NI, NA
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Methionine aminopeptidase (EC 3.4.11.18)	protein	279	28% helix, 28% strand	Q9KPV1

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

5 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	122	0.57	0.84	21	empty
2	112	0.54	0.83	19	NI
3	337	0.53	0.74	39	empty
4	215	0.45	0.73	34	GOL
5	63	0.27	0.72	16	empty

Interfaces

1 interface between chains.

A–B · 342 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6KSG · Vibrio cholerae Methionine Aminopeptidase in holo form · 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 Q9KPV1
Elsewhere: RCSB PDB 6KSG · PDBe 6KSG · UniProt Q9KPV1

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