Research workbench
Hexagonal form P6122 of the aquifex aeolicus nucleoside diphosphate kinase (first stage of radiation damage)
Analyse Hexagonal form P6122 of the aquifex aeolicus nucleoside diphosphate kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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