MolNFT v1 · #9120 · protein + DNA
Crystal structure of cenp-B(1-129) complexed with the cenp- B box DNA
1HLV · Cenp-B box DNA: “Crystal structure of cenp-B(1-129) complexed with the cenp- B box DNA”. X-ray diffraction, 3 pockets (best druggability 0.34). MolNFT v1 #9120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HLV
- Type
- protein + DNA
- Length
- 173 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cenp-B box DNA; Major centromere autoantigen B
- UniProt
- P07199
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cenp-B box DNA | dna | 21 | — | — |
| C | Cenp-B box DNA | dna | 21 | — | — |
| A | Major centromere autoantigen B | protein | 131 | 67% helix, 0% strand | P07199 |
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 | 97 | 0.34 | 0.74 | 19 | empty |
| 2 | 56 | 0.30 | 0.76 | 13 | empty |
| 3 | 51 | 0.23 | 0.72 | 10 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1172 Ų buried · 31 hydrogen bonds · protein-nucleic
- B–C · 921 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- C–A · 884 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 1HLV · Crystal structure of cenp-B(1-129) complexed with the cenp-B box DNA · the same entry in another collection · chain C against C, TM-score 1.00
- P07199 · AlphaFold monomer V2.0 prediction for major centromere autoantigen B (P07199) · a predicted model of the same protein · chain A against A, TM-score 0.77
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 P07199
- Elsewhere: RCSB PDB 1HLV · PDBe 1HLV · UniProt P07199
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