MolNFT v1 · #112335 · protein
Crystal structure of leucine aminopeptidase from helicobacter pylori
4ZI6 · Cytosol aminopeptidase: “Crystal structure of leucine aminopeptidase from helicobacter pylori”. X-ray diffraction, 3 ligands (BCT, ZN, NA), 20 pockets (best druggability 0.73). MolNFT v1 #112335 on GenesisL1: 3D structure, binding…
- PDB
- 4ZI6
- Type
- protein
- Length
- 2,887 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosol aminopeptidase
- EC
- 3.4.11.1, 3.4.11.10
- UniProt
- O25294
- Ligands
- BCT, ZN, NA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 484 | 38% helix, 22% strand | O25294 |
| B | Cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 480 | 39% helix, 23% strand | O25294 |
| C | Cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 481 | 38% helix, 22% strand | O25294 |
| D | Cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 479 | 39% helix, 23% strand | O25294 |
| E | Cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 483 | 39% helix, 22% strand | O25294 |
| F | Cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 480 | 38% helix, 22% strand | O25294 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.73 | 0.80 | 63 | BCT, NA |
| 2 | 563 | 0.72 | 0.81 | 52 | NA |
| 3 | 585 | 0.72 | 0.80 | 54 | NA |
| 4 | 587 | 0.72 | 0.80 | 51 | BCT, NA |
| 5 | 952 | 0.72 | 0.76 | 116 | empty |
Interfaces
12 interfaces between chains.
- A–E · 1378 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 1357 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1341 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1144 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1141 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4ZI6 · Crystal structure of leucine aminopeptidase from Helicobacter pylori · the same entry in another collection · chain F against F, TM-score 1.00
- O25294 · AlphaFold monomer V2.0 prediction for cytosol aminopeptidase (O25294) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O25294
- Elsewhere: RCSB PDB 4ZI6 · PDBe 4ZI6 · UniProt O25294
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