MolNFT v1 · #154103 · protein
Crystal structure B of CENAP1-H2A-H2B complex
6K09 · Nucleosome assembly protein: “Crystal structure B of CENAP1-H2A-H2B complex”. X-ray diffraction, 5 pockets (best druggability 0.76). MolNFT v1 #154103 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K09
- Type
- protein
- Length
- 715 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleosome assembly protein; Histone H2B 1,HISTONE H2A
- UniProt
- Q19007, P04255, P09588
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleosome assembly protein | protein | 267 | 46% helix, 16% strand | Q19007 |
| B | Nucleosome assembly protein | protein | 267 | 47% helix, 15% strand | Q19007 |
| D | Histone H2B 1,HISTONE H2A | protein | 181 | 69% helix, 4% strand | P04255, P09588 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.76 | 0.80 | 75 | empty |
| 2 | 683 | 0.71 | 0.78 | 65 | empty |
| 3 | 151 | 0.44 | 0.75 | 17 | empty |
| 4 | 54 | 0.37 | 0.79 | 16 | empty |
| 5 | 56 | 0.27 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4570 Ų buried · 67 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 368 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6K09 · Crystal structure B of ceNAP1-H2A-H2B complex · the same entry in another collection · chain A against A, TM-score 1.00
- P09588 · AlphaFold monomer V2.0 prediction for histone H2A (P09588) · a predicted model of the same protein · chain D against A, TM-score 0.48
- P04255 · AlphaFold monomer V2.0 prediction for histone H2B 1 (P04255) · a predicted model of the same protein · chain D against A, TM-score 0.47
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 Q19007
- Every structure of UniProt P04255
- Every structure of UniProt P09588
- Elsewhere: RCSB PDB 6K09 · PDBe 6K09 · UniProt Q19007 · UniProt P04255 · UniProt P09588
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