Research workbench
M. tuberculosis metap with bengamide analog Y08, in mn form
Analyse M. tuberculosis metap with bengamide analog Y08, in mn form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PKC
- Type
- protein
- Length
- 281 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
- Y08, MN
- Pockets
- 1 · best druggability 0.59
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 | 281 | 25% helix, 24% strand | P0A5J2 |
Ligands and binding sites
- Y08 · (E,2R,3R,4S,5R)-N-[[(3S)-1-cyclopropylcarbonylpiperidin-3-yl]methyl]-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.59 | 0.81 | 29 | Y08 |
Compared structures
- 3PKC · M. tuberculosis MetAP with bengamide analog Y08, in Mn 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 3PKC · PDBe 3PKC · UniProt P0A5J2
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