MolNFT v1 · #163829 · protein + DNA
CLASS1: cenp-a nucleosome in complex with cenp-C central region
6SEG · Histone H3-like centromeric protein a: “CLASS1: cenp-a nucleosome in complex with cenp-C central region”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #163829 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SEG
- Type
- protein + DNA
- Length
- 1,018 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3-like centromeric protein a; Histone H4; Histone H2A type 2-a; Histone H2B type…
- UniProt
- P49450, P62805, Q6FI13, P62807
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 8 distinct chains · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3-like centromeric protein a | protein | 95 | 65% helix, 4% strand | P49450 |
| B, F | Histone H4 | protein | 78 | 63% helix, 9% strand | P62805 |
| C | Histone H2A type 2-a | protein | 96 | 55% helix, 6% strand | Q6FI13 |
| D | Histone H2B type 1-C/E/F/G/I | protein | 92 | 74% helix, 3% strand | P62807 |
| G | Histone H2A type 2-a | protein | 104 | 52% helix, 6% strand | Q6FI13 |
| H | Histone H2B type 1-C/E/F/G/I | protein | 90 | 73% helix, 3% strand | P62807 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.85 | 0.87 | 97 | empty |
| 2 | 316 | 0.78 | 0.89 | 46 | empty |
| 3 | 453 | 0.65 | 0.78 | 43 | empty |
| 4 | 233 | 0.65 | 0.84 | 32 | empty |
| 5 | 364 | 0.64 | 0.79 | 24 | empty |
Interfaces
38 interfaces between chains.
- I–J · 6503 Ų buried · 490 hydrogen bonds · nucleic-nucleic
- C–D · 2650 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2604 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2592 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2558 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6SEG · Class1: CENP-A nucleosome in complex with CENP-C central region · the same entry in another collection · chain J against J, TM-score 1.00
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q6FI13 · AlphaFold monomer V2.0 prediction for histone H2A type 2-a (Q6FI13) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P49450
- Every structure of UniProt P62805
- Every structure of UniProt Q6FI13
- Every structure of UniProt P62807
- Elsewhere: RCSB PDB 6SEG · PDBe 6SEG · UniProt P49450 · UniProt P62805 · UniProt Q6FI13 · UniProt P62807
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