MolNFT v1 · #75240 · protein

M. tuberculosis metap with bengamide analog Y10, in ni form

3PKE · Methionine aminopeptidase: “M. tuberculosis metap with bengamide analog Y10, in ni form”. X-ray diffraction, 4 ligands (Y10, NI, CL), 2 pockets (best druggability 0.61). MolNFT v1 #75240 on GenesisL1: 3D structure, binding sites and…

PDB: 3PKE
Type: protein
Length: 284 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine aminopeptidase
EC: 3.4.11.18
UniProt: P0A5J2
Ligands: Y10, NI, CL, SO4
Pockets: 2 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionine aminopeptidase (EC 3.4.11.18)	protein	284	25% helix, 24% strand	P0A5J2

Ligands and binding sites

Y10 · (E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide · ligand · chains A
NI · Nickel (II) ion · metal · 2 copies · chains A
CL · Chloride ion · ion · chains A
SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	185	0.61	0.83	32	Y10
2	61	0.32	0.76	17	empty

Compared structures

3PKE · M. tuberculosis MetAP with bengamide analog Y10, in Ni 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 P0A5J2
Elsewhere: RCSB PDB 3PKE · PDBe 3PKE · UniProt P0A5J2

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