MolNFT v1 · #154094 · protein
Crystal structure a of CENAP1-H2A-H2B complex
6K00 · Nucleosome assembly protein: “Crystal structure a of CENAP1-H2A-H2B complex”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #154094 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K00
- Type
- protein
- Length
- 712 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
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleosome assembly protein | protein | 263 | 47% helix, 17% strand | Q19007 |
| B | Nucleosome assembly protein | protein | 269 | 48% helix, 16% strand | Q19007 |
| D | Histone H2B 1,HISTONE H2A | protein | 180 | 68% helix, 3% strand | P04255, P09588 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.76 | 0.82 | 65 | empty |
| 2 | 312 | 0.67 | 0.82 | 54 | empty |
| 3 | 268 | 0.53 | 0.75 | 24 | empty |
| 4 | 166 | 0.45 | 0.75 | 20 | empty |
| 5 | 58 | 0.29 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4539 Ų buried · 64 hydrogen bonds · protein-protein
- A–D · 527 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 388 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6K00 · Crystal structure A 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 6K00 · PDBe 6K00 · UniProt Q19007 · UniProt P04255 · UniProt P09588
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