MolNFT v1 · #164948 · protein + DNA
Cenp-a nucleosome core particle with 145 base pairs of the widom 601 sequence by cryo-EM
6TEM · Histone H3-like centromeric protein a: “Cenp-a nucleosome core particle with 145 base pairs of the widom 601 sequence by cryo-EM”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #164948 on GenesisL1: 3D…
- PDB
- 6TEM
- Type
- protein + DNA
- Length
- 989 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; Histone H2B 1.1; Widom…
- UniProt
- P49450, P62799, Q6AZJ8, P02281
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 10 distinct chains · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3-like centromeric protein a | protein | 88 | 70% helix, 2% strand | P49450 |
| B | Histone H4 | protein | 79 | 58% helix, 5% strand | P62799 |
| C | Histone H2A | protein | 104 | 48% helix, 5% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 95 | 72% helix, 4% strand | P02281 |
| E | Histone H3-like centromeric protein a | protein | 89 | 69% helix, 2% strand | P49450 |
| F | Histone H4 | protein | 78 | 58% helix, 4% strand | P62799 |
| G | Histone H2A | protein | 103 | 52% helix, 6% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 93 | 74% helix, 4% strand | P02281 |
| I | Widom 601 DNA (145-mer, sense) | dna | 130 | — | — |
| J | Widom 601 DNA (145-mer, antisense) | dna | 130 | — | — |
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 | 634 | 0.78 | 0.84 | 66 | empty |
| 2 | 611 | 0.76 | 0.83 | 72 | empty |
| 3 | 238 | 0.74 | 0.88 | 42 | empty |
| 4 | 750 | 0.68 | 0.76 | 53 | empty |
| 5 | 225 | 0.65 | 0.84 | 28 | empty |
Interfaces
37 interfaces between chains.
- I–J · 5980 Ų buried · 496 hydrogen bonds · nucleic-nucleic
- G–H · 2590 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2578 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 2535 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2493 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6TEM · CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM · the same entry in another collection · chain J against J, TM-score 1.00
- P49450 · AlphaFold monomer V2.0 prediction for histone H3-like centromeric protein a (P49450) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 6TEM · PDBe 6TEM · UniProt P49450 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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