MolNFT v1 · #58699 · protein
Crystal structure of the NM23-H2 transcription factor complex with dinucleotide D(AG)
3BBB · Nucleoside diphosphate kinase B: “Crystal structure of the NM23-H2 transcription factor complex with dinucleotide D(AG)”. X-ray diffraction, 2 ligands (DG, DA), 15 pockets (best druggability 0.85). MolNFT v1 #58699 on GenesisL1: 3D…
- PDB
- 3BBB
- Type
- protein
- Length
- 900 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
- Ligands
- DG, DA
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F | Nucleoside diphosphate kinase B (EC 2.7.4.6) | protein | 151 | 46% helix, 17% strand | P22392 |
| C, E | Nucleoside diphosphate kinase B (EC 2.7.4.6) | protein | 148 | 49% helix, 16% strand | P22392 |
Ligands and binding sites
- DG · 2'-deoxyguanosine-5'-monophosphate · ligand · 4 copies · chains B, C, E, F
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · 2 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.85 | 0.91 | 57 | empty |
| 2 | 524 | 0.85 | 0.91 | 57 | empty |
| 3 | 861 | 0.84 | 0.86 | 75 | empty |
| 4 | 495 | 0.84 | 0.90 | 57 | empty |
| 5 | 240 | 0.55 | 0.77 | 52 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1089 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 1057 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 1046 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 835 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 827 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3BBB · Crystal structure of the NM23-H2 transcription factor complex with dinucleotide d(AG) · the same entry in another collection · chain F against F, 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 3BBB · PDBe 3BBB · UniProt P22392
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