MolNFT v1 · #163819 · protein + DNA
CLASS2 : cenp-a nucleosome in complex with cenp-C central region
6SE6 · Histone H3-like centromeric protein a: “CLASS2 : cenp-a nucleosome in complex with cenp-C central region”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #163819 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SE6
- Type
- protein + DNA
- Length
- 1,061 residues
- Chains
- 11
- 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, Q03188
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 10 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3-like centromeric protein a | protein | 98 | 63% helix, 4% strand | P49450 |
| B | Histone H4 | protein | 82 | 62% helix, 6% strand | P62805 |
| C | Histone H2A type 2-a | protein | 101 | 55% helix, 7% strand | Q6FI13 |
| D | Histone H2B type 1-C/E/F/G/I | protein | 92 | 73% helix, 4% strand | P62807 |
| F | Histone H4 | protein | 84 | 55% helix, 7% strand | P62805 |
| G | Histone H2A type 2-a | protein | 108 | 52% helix, 5% strand | Q6FI13 |
| H | Histone H2B type 1-C/E/F/G/I | protein | 90 | 77% helix, 4% strand | P62807 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| V | Centromere protein C | protein | 18 | 0% helix, 0% strand | Q03188 |
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 | 683 | 0.82 | 0.86 | 101 | empty |
| 2 | 412 | 0.81 | 0.90 | 50 | empty |
| 3 | 368 | 0.77 | 0.87 | 52 | empty |
| 4 | 1100 | 0.72 | 0.76 | 72 | empty |
| 5 | 343 | 0.66 | 0.81 | 28 | empty |
Interfaces
42 interfaces between chains.
- I–J · 6516 Ų buried · 575 hydrogen bonds · nucleic-nucleic
- G–H · 2655 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2619 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2617 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2573 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6SE6 · Class2 : CENP-A nucleosome in complex with CENP-C central region · the same entry in another collection · chain V against V, 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 P62805
- Every structure of UniProt Q6FI13
- Every structure of UniProt P62807
- Every structure of UniProt Q03188
- Elsewhere: RCSB PDB 6SE6 · PDBe 6SE6 · UniProt P49450 · UniProt P62805 · UniProt Q6FI13 · UniProt P62807 · UniProt Q03188
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