Research workbench
Crystal structure of aminopeptidase a from neisseria gonorrhoeae
Analyse Crystal structure of aminopeptidase a from neisseria gonorrhoeae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D1X
- Type
- protein
- Length
- 2,809 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable cytosol aminopeptidase
- EC
- 3.4.11.1, 3.4.11.10
- UniProt
- B4RJ22
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Probable cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 468 | 39% helix, 22% strand | B4RJ22 |
| C | Probable cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 467 | 39% helix, 22% strand | B4RJ22 |
| D, F | Probable cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 469 | 39% helix, 23% strand | B4RJ22 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- TAR · D(-)-tartaric acid · additive · 6 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.72 | 0.76 | 100 | MN, CL |
| 2 | 734 | 0.69 | 0.77 | 55 | empty |
| 3 | 699 | 0.68 | 0.77 | 55 | empty |
| 4 | 645 | 0.68 | 0.77 | 54 | empty |
| 5 | 645 | 0.68 | 0.77 | 53 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1012 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1010 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 996 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 982 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 974 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 8D1X · Crystal Structure of aminopeptidase A from Neisseria gonorrhoeae · 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 B4RJ22
- Elsewhere: RCSB PDB 8D1X · PDBe 8D1X · UniProt B4RJ22
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.