Research workbench
Cryo-EM structure of ncp-6-4PP(-1)-UV-ddb
Analyse Cryo-EM structure of ncp-6-4PP(-1)-UV-ddb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R8Y
- Type
- protein + DNA
- Length
- 2,285 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; Human…
- UniProt
- P68431, P62805, P04908, P06899, Q16531, Q92466
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 9 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.1 | protein | 101 | 65% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 86 | 57% helix, 8% strand | P62805 |
| C, G | Histone H2A type 1-B/E | protein | 117 | 50% helix, 5% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 97 | 72% helix, 4% strand | P06899 |
| F | Histone H4 | protein | 82 | 60% helix, 6% strand | P62805 |
| I | Human alpha-satellite DNA (145-mer) | dna | 145 | — | — |
| J | Human alpha-satellite DNA (145-mer) with a 6-4PP at positions 95-96 | dna | 144 | — | — |
| K | DNA damage-binding protein 1 | protein | 825 | 8% helix, 50% strand | Q16531 |
| L | DNA damage-binding protein 2 | protein | 373 | 7% helix, 37% strand | Q92466 |
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 | 510 | 0.81 | 0.88 | 70 | empty |
| 2 | 1026 | 0.81 | 0.82 | 112 | empty |
| 3 | 513 | 0.78 | 0.85 | 44 | empty |
| 4 | 479 | 0.78 | 0.86 | 58 | empty |
| 5 | 305 | 0.76 | 0.88 | 46 | empty |
Interfaces
40 interfaces between chains.
- I–J · 6147 Ų buried · 427 hydrogen bonds · nucleic-nucleic
- K–L · 2834 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2636 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2613 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2562 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6R8Y · Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB · the same entry in another collection · chain L against L, 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt Q16531
- Every structure of UniProt Q92466
- Elsewhere: RCSB PDB 6R8Y · PDBe 6R8Y · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt Q16531 · UniProt Q92466
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