Research workbench
Crystal structure of the enterococcus faecalis methionine aminopeptidase apo form
Analyse Crystal structure of the enterococcus faecalis methionine aminopeptidase apo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TB5
- Type
- protein
- Length
- 715 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase
- EC
- 3.4.11.18
- UniProt
- C7VIN6
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methionine aminopeptidase (EC 3.4.11.18) | protein | 254 | 29% helix, 26% strand | C7VIN6 |
| C | Methionine aminopeptidase (EC 3.4.11.18) | protein | 207 | 33% helix, 29% strand | C7VIN6 |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.70 | 0.79 | 62 | empty |
| 2 | 161 | 0.66 | 0.86 | 28 | CIT |
| 3 | 139 | 0.65 | 0.87 | 26 | CIT |
| 4 | 116 | 0.39 | 0.75 | 22 | empty |
| 5 | 86 | 0.33 | 0.73 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 628 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 517 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3TB5 · Crystal Structure of the Enterococcus faecalis Methionine aminopeptidase apo 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 C7VIN6
- Elsewhere: RCSB PDB 3TB5 · PDBe 3TB5 · UniProt C7VIN6
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