MolNFT v1 · #138247 · protein + DNA
Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5
5WCU · Histone H3: “Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #138247 on GenesisL1: 3D structure, binding sites and pockets…
- 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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