MolNFT v1 · #109628 · protein
De novo crystal structure of the pyrococcus furiosus TET3 aminopeptidase
4X8I · Lysyl aminopeptidase: “De novo crystal structure of the pyrococcus furiosus TET3 aminopeptidase”. X-ray diffraction, 5 ligands (DO3, GD, ZN), 10 pockets (best druggability 0.73). MolNFT v1 #109628 on GenesisL1: 3D structure, binding…
- PDB
- 4X8I
- Type
- protein
- Length
- 1,012 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl aminopeptidase
- EC
- 3.4.11.15
- UniProt
- Q8TZW4
- Ligands
- DO3, GD, ZN, CO, CL
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysyl aminopeptidase (EC 3.4.11.15) | protein | 337 | 28% helix, 27% strand | Q8TZW4 |
| B | Lysyl aminopeptidase (EC 3.4.11.15) | protein | 338 | 29% helix, 27% strand | Q8TZW4 |
Ligands and binding sites
- DO3 · 10-((2R)-2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane 1,4,7-triacetic acid · ligand · chains C
- GD · Gadolinium atom · metal · 11 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CO · Cobalt (II) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.73 | 0.87 | 36 | empty |
| 2 | 307 | 0.57 | 0.77 | 35 | CL |
| 3 | 341 | 0.56 | 0.75 | 44 | empty |
| 4 | 292 | 0.54 | 0.76 | 32 | CL |
| 5 | 278 | 0.52 | 0.75 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1168 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1135 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1122 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4X8I · de novo crystal structure of the Pyrococcus Furiosus TET3 aminopeptidase · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TZW4 · AlphaFold monomer V2.0 prediction for lysyl aminopeptidase (Q8TZW4) · a predicted model of the same protein · 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 Q8TZW4
- Elsewhere: RCSB PDB 4X8I · PDBe 4X8I · UniProt Q8TZW4
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