Research workbench
Structure of the human ccandeltat cenp-a alpha-satellite complex
Analyse Structure of the human ccandeltat cenp-a alpha-satellite complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YYH
- Type
- protein + DNA
- Length
- 3,679 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3-like centromeric protein a; Histone H4; Histone H2A type 1-C; Histone H2B type…
- UniProt
- P49450, P62805, Q93077, P62807, Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q71F23, Q03188
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 22 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3-like centromeric protein a | protein | 99 | 68% helix, 4% strand | P49450 |
| B | Histone H4 | protein | 78 | 59% helix, 8% strand | P62805 |
| C | Histone H2A type 1-C | protein | 98 | 59% helix, 5% strand | Q93077 |
| D, h | Histone H2B type 1-C/E/F/G/I | protein | 92 | 75% helix, 3% strand | P62807 |
| E | Histone H3-like centromeric protein a | protein | 94 | 65% helix, 4% strand | P49450 |
| F | Histone H4 | protein | 80 | 60% helix, 8% strand | P62805 |
| G | Histone H2A type 1-C | protein | 103 | 54% helix, 6% strand | Q93077 |
| H | Centromere protein H | protein | 171 | 85% helix, 0% strand | Q9H3R5 |
| I | Centromere protein I | protein | 543 | 67% helix, 1% strand | Q92674 |
| J | DNA (171-mer) | dna | 153 | — | — |
| K | Centromere protein K | protein | 217 | 71% helix, 4% strand | Q9BS16 |
| L | Centromere protein L | protein | 297 | 39% helix, 25% strand | Q8N0S6 |
| M | Centromere protein M | protein | 172 | 38% helix, 19% strand | Q9NSP4 |
| N | Centromere protein N | protein | 297 | 42% helix, 22% strand | Q96H22 |
| O | Centromere protein O | protein | 210 | 44% helix, 21% strand | Q9BU64 |
| P | Centromere protein P | protein | 219 | 42% helix, 32% strand | Q6IPU0 |
| Q | Centromere protein Q | protein | 189 | 72% helix, 1% strand | Q7L2Z9 |
| R | Centromere protein R | protein | 80 | 74% helix, 0% strand | Q13352 |
| U | Centromere protein U | protein | 165 | 88% helix, 0% strand | Q71F23 |
| k | Centromere protein C | protein | 21 | 0% helix, 10% strand | Q03188 |
| l | Centromere protein C | protein | 57 | 19% helix, 11% strand | Q03188 |
| i | DNA (171-mer) | dna | 152 | — | — |
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 | 1049 | 0.87 | 0.88 | 126 | empty |
| 2 | 812 | 0.86 | 0.88 | 89 | empty |
| 3 | 683 | 0.83 | 0.87 | 59 | empty |
| 4 | 616 | 0.82 | 0.87 | 59 | empty |
| 5 | 652 | 0.81 | 0.86 | 75 | empty |
Interfaces
77 interfaces between chains.
- J–i · 6701 Ų buried · 553 hydrogen bonds · nucleic-nucleic
- H–K · 4308 Ų buried · 21 hydrogen bonds · protein-protein
- Q–U · 3162 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 2592 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 2590 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 7YYH · Structure of the human CCANdeltaT CENP-A alpha-satellite complex · the same entry in another collection · chain H against H, 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 P49450
- Every structure of UniProt P62805
- Every structure of UniProt Q93077
- Every structure of UniProt P62807
- Every structure of UniProt Q9H3R5
- Every structure of UniProt Q92674
- Every structure of UniProt Q9BS16
- Every structure of UniProt Q8N0S6
- Every structure of UniProt Q9NSP4
- Every structure of UniProt Q96H22
- Every structure of UniProt Q9BU64
- Every structure of UniProt Q6IPU0
- Every structure of UniProt Q7L2Z9
- Every structure of UniProt Q13352
- Every structure of UniProt Q71F23
- Every structure of UniProt Q03188
- Elsewhere: RCSB PDB 7YYH · PDBe 7YYH · UniProt P49450 · UniProt P62805 · UniProt Q93077 · UniProt P62807 · UniProt Q9H3R5 · UniProt Q92674 · UniProt Q9BS16 · UniProt Q8N0S6 · UniProt Q9NSP4 · UniProt Q96H22 · UniProt Q9BU64 · UniProt Q6IPU0 · UniProt Q7L2Z9 · UniProt Q13352 · UniProt Q71F23 · UniProt Q03188
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