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Crystal structure of pf-MAP(1-292)-C

Analyse Crystal structure of pf-MAP(1-292)-C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DFI
Type: protein
Length: 602 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine aminopeptidase
EC: 3.4.11.18
UniProt: P56218
Ligands: CO
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Methionine aminopeptidase (EC 3.4.11.18)	protein	301	32% helix, 27% strand	P56218

Ligands and binding sites

CO · Cobalt (II) ion · metal · 6 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	91	0.78	0.98	23	CO
2	84	0.76	0.98	20	CO
3	128	0.46	0.77	20	empty
4	95	0.43	0.78	14	empty
5	106	0.38	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 1389 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

2DFI · Crystal structure of Pf-MAP(1-292)-C · the same entry in another collection · chain A against A, TM-score 1.00
P56218 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase (P56218) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P56218
Elsewhere: RCSB PDB 2DFI · PDBe 2DFI · UniProt P56218

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