Research workbench
Crystal structure of reconstructed bacterial ancestral ndk, BAC1
Analyse Crystal structure of reconstructed bacterial ancestral ndk, BAC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VVU
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 139 | 45% helix, 17% strand | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.47 | 0.77 | 24 | empty |
| 2 | 146 | 0.45 | 0.76 | 23 | empty |
| 3 | 132 | 0.39 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3VVU · Crystal structure of reconstructed bacterial ancestral NDK, Bac1 · the same entry in another collection · 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
- Elsewhere: RCSB PDB 3VVU · PDBe 3VVU
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