MolNFT v1 · #109322 · protein
APN1 from anopheles gambiae
4WZ9 · AGAP004809-pa: “APN1 from anopheles gambiae”. X-ray diffraction, 2 ligands (ZN, CU), 14 pockets (best druggability 0.81). MolNFT v1 #109322 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WZ9
- Type
- protein
- Length
- 1,777 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AGAP004809-pa; Ala-ala-ala-lys-ala; Ala-ala-lys
- UniProt
- Q7Q2T8
- Ligands
- ZN, CU
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AGAP004809-pa | protein | 882 | 44% helix, 21% strand | Q7Q2T8 |
| B | AGAP004809-pa | protein | 887 | 44% helix, 21% strand | Q7Q2T8 |
| M | Ala-ala-ala-lys-ala | protein | 5 | 0% helix, 20% strand | — |
| N | Ala-ala-lys | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, M, B, N
- CU · Copper (II) ion · metal · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.81 | 0.83 | 104 | empty |
| 2 | 930 | 0.75 | 0.79 | 97 | empty |
| 3 | 1086 | 0.73 | 0.76 | 85 | empty |
| 4 | 1096 | 0.71 | 0.75 | 98 | empty |
| 5 | 193 | 0.50 | 0.76 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1060 Ų buried · 12 hydrogen bonds · protein-protein
- A–M · 313 Ų buried · 8 hydrogen bonds · protein-protein
- B–N · 294 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 Q7Q2T8
- Elsewhere: RCSB PDB 4WZ9 · PDBe 4WZ9 · UniProt Q7Q2T8
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