Research workbench
Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5
Analyse Crystal structure of 167 bp nucleosome bound to the globular domain of linker… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WCU
- Type
- protein + DNA
- Length
- 2,316 residues
- Chains
- 22
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (167-mer); Histone H5
- UniProt
- P02299, P84040, P84051, P02283, P02259
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 11 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | Histone H3 | protein | 98 | 67% helix, 4% strand | P02299 |
| B, L | Histone H4 | protein | 80 | 64% helix, 9% strand | P84040 |
| C, M | Histone H2A | protein | 104 | 55% helix, 6% strand | P84051 |
| D, N | Histone H2B | protein | 94 | 74% helix, 3% strand | P02283 |
| E, O | Histone H3 | protein | 97 | 67% helix, 4% strand | P02299 |
| F, P | Histone H4 | protein | 82 | 62% helix, 9% strand | P84040 |
| G, Q | Histone H2A | protein | 103 | 55% helix, 7% strand | P84051 |
| H, R | Histone H2B | protein | 93 | 75% helix, 4% strand | P02283 |
| I, S | DNA (167-mer) | dna | 164 | — | — |
| J, T | DNA (167-mer) | dna | 167 | — | — |
| U, V | Histone H5 | protein | 76 | 47% helix, 8% strand | P02259 |
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 | 949 | 0.82 | 0.84 | 92 | empty |
| 2 | 781 | 0.80 | 0.84 | 69 | empty |
| 3 | 546 | 0.77 | 0.84 | 51 | empty |
| 4 | 397 | 0.75 | 0.86 | 54 | empty |
| 5 | 356 | 0.73 | 0.85 | 48 | empty |
Interfaces
78 interfaces between chains.
- S–T · 7634 Ų buried · 645 hydrogen bonds · nucleic-nucleic
- I–J · 7530 Ų buried · 631 hydrogen bonds · nucleic-nucleic
- M–N · 2744 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2698 Ų buried · 25 hydrogen bonds · protein-protein
- Q–R · 2680 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5WCU · Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 · the same entry in another collection · chain K against K, 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 P02299
- Every structure of UniProt P84040
- Every structure of UniProt P84051
- Every structure of UniProt P02283
- Every structure of UniProt P02259
- Elsewhere: RCSB PDB 5WCU · PDBe 5WCU · UniProt P02299 · UniProt P84040 · UniProt P84051 · UniProt P02283 · UniProt P02259
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