MolNFT v1 · #84735 · protein
Hexagonal form P6122 of the aquifex aeolicus nucleoside diphosphate kinase (first stage of radiation damage)
3ZTR: “Hexagonal form P6122 of the aquifex aeolicus nucleoside diphosphate kinase (first stage of radiation damage)”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #84735 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ZTR
- Type
- protein
- Length
- 1,692 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- O67528
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 141 | 48% helix, 20% strand | O67528 |
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 | 922 | 0.85 | 0.86 | 69 | empty |
| 2 | 912 | 0.85 | 0.86 | 70 | empty |
| 3 | 914 | 0.85 | 0.86 | 69 | empty |
| 4 | 813 | 0.74 | 0.79 | 65 | empty |
| 5 | 1120 | 0.71 | 0.75 | 100 | empty |
Interfaces
23 interfaces between chains.
- I–J · 757 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 757 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 756 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 753 Ų buried · 5 hydrogen bonds · protein-protein
- K–L · 750 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3ZTR · Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FIRST STAGE… · the same entry in another collection · chain L against L, 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 O67528
- Elsewhere: RCSB PDB 3ZTR · PDBe 3ZTR · UniProt O67528
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