Research workbench
Crystal structure of R88A mutant of the NM23-H2 transcription factor
Analyse Crystal structure of R88A mutant of the NM23-H2 transcription factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BBC
- Type
- protein
- Length
- 906 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase B
- EC
- 2.7.4.6
- UniProt
- P22392
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleoside diphosphate kinase B (EC 2.7.4.6) | protein | 151 | 48% helix, 16% strand | P22392 |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.88 | 0.90 | 126 | empty |
| 2 | 514 | 0.85 | 0.91 | 61 | empty |
| 3 | 481 | 0.85 | 0.91 | 58 | empty |
| 4 | 214 | 0.48 | 0.75 | 30 | empty |
| 5 | 197 | 0.47 | 0.75 | 31 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1100 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1068 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1048 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 839 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 830 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3BBC · Crystal structure of R88A mutant of the NM23-H2 transcription factor · the same entry in another collection · chain C against C, TM-score 1.00
- P22392 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase B (P22392) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P22392
- Elsewhere: RCSB PDB 3BBC · PDBe 3BBC · UniProt P22392
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