MolNFT v1 · #174512 · protein + DNA
The cryo-EM structure of cenp-a nucleosome in complex with cenp-C peptide and cenp-N N-terminal domain
7BXT · Histone H3,HISTONE H3-like centromeric protein a: “The cryo-EM structure of cenp-a nucleosome in complex with cenp-C peptide and cenp-N N-terminal domain”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #174512…
- PDB
- 7BXT
- Type
- protein + DNA
- Length
- 1,491 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3,HISTONE H3-like centromeric protein a; Histone H4; Histone H2A type 1-B/E…
- UniProt
- Q6XXM1, P62805, P04908, Q16778, O57392, Q1T765
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3,HISTONE H3-like centromeric protein a | protein | 103 | 58% helix, 2% strand | Q6XXM1 |
| B, F | Histone H4 | protein | 79 | 59% helix, 6% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 107 | 44% helix, 4% strand | P04908 |
| D, H | Histone H2B type 2-E | protein | 94 | 67% helix, 2% strand | Q16778 |
| G | Histone H2A type 1-B/E | protein | 108 | 44% helix, 6% strand | P04908 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| K, L | Cenp-C | protein | 19 | 0% helix, 0% strand | O57392 |
| M, N | Maltodextrin-binding PROTEIN,CENTROMERE protein N | protein | 198 | 37% helix, 20% strand | Q1T765 |
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 | 882 | 0.87 | 0.90 | 104 | empty |
| 2 | 962 | 0.85 | 0.87 | 100 | empty |
| 3 | 453 | 0.81 | 0.89 | 62 | empty |
| 4 | 459 | 0.79 | 0.87 | 55 | empty |
| 5 | 305 | 0.74 | 0.87 | 33 | empty |
Interfaces
59 interfaces between chains.
- I–J · 6394 Ų buried · 648 hydrogen bonds · nucleic-nucleic
- E–F · 2638 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2636 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2587 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2582 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7BXT · The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N… · the same entry in another collection · chain N against N, TM-score 1.00
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 Q6XXM1
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt Q16778
- Every structure of UniProt O57392
- Every structure of UniProt Q1T765
- Elsewhere: RCSB PDB 7BXT · PDBe 7BXT · UniProt Q6XXM1 · UniProt P62805 · UniProt P04908 · UniProt Q16778 · UniProt O57392 · UniProt Q1T765
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