Research workbench
Crystal structure of TMPEP1050 aminopeptidase with its metal cofactors
Analyse Crystal structure of TMPEP1050 aminopeptidase with its metal cofactors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NW5
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase
- UniProt
- Q9X0E0
- Ligands
- ZN, CO, SO4, OH
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aminopeptidase | protein | 331 | 29% helix, 29% strand | Q9X0E0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 25 copies · chains A, B, C, D
- OH · Hydroxide ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.80 | 0.82 | 78 | empty |
| 2 | 457 | 0.70 | 0.81 | 44 | empty |
| 3 | 91 | 0.49 | 0.83 | 20 | SO4 |
| 4 | 112 | 0.49 | 0.81 | 23 | empty |
| 5 | 111 | 0.49 | 0.80 | 23 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 2024 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1109 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1108 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1107 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NW5 · Crystal structure of TmPep1050 aminopeptidase with its metal cofactors · 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 Q9X0E0
- Elsewhere: RCSB PDB 6NW5 · PDBe 6NW5 · UniProt Q9X0E0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.