Research workbench
Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, HTH2B
Analyse Crystal structure of nucleosome particle in the presence of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GT3
- Type
- protein + DNA
- Length
- 1,051 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-D; Histone H2B type 1-a; DNA (146-mer)
- UniProt
- P68431, P62805, P20671, Q96A08
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 9 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 98 | 63% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 81 | 60% helix, 9% strand | P62805 |
| C | Histone H2A type 1-D | protein | 106 | 57% helix, 7% strand | P20671 |
| D | Histone H2B type 1-a | protein | 95 | 73% helix, 4% strand | Q96A08 |
| E | Histone H3.1 | protein | 99 | 63% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 85 | 59% helix, 8% strand | P62805 |
| G | Histone H2A type 1-D | protein | 103 | 57% helix, 7% strand | P20671 |
| H | Histone H2B type 1-a | protein | 92 | 75% helix, 4% strand | Q96A08 |
| I, J | DNA (146-mer) | dna | 146 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains E, F, G, H, I, J
- CL · Chloride ion · ion · 5 copies · chains I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 587 | 0.78 | 0.84 | 73 | empty |
| 2 | 471 | 0.75 | 0.84 | 56 | empty |
| 3 | 350 | 0.74 | 0.86 | 47 | empty |
| 4 | 530 | 0.70 | 0.80 | 43 | empty |
| 5 | 808 | 0.70 | 0.76 | 55 | empty |
Interfaces
38 interfaces between chains.
- I–J · 6413 Ų buried · 506 hydrogen bonds · nucleic-nucleic
- C–D · 2702 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2644 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2596 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2575 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5GT3 · Crystal structure of nucleosome particle in the presence of human testis-specific histone… · the same entry in another collection · chain J against J, TM-score 1.00
- Q96A08 · AlphaFold monomer V2.0 prediction for histone H2B type 1-a (Q96A08) · a predicted model of the same protein · chain H against A, TM-score 0.97
- P20671 · AlphaFold monomer V2.0 prediction for histone H2A type 1-D (P20671) · a predicted model of the same protein · chain G against A, TM-score 0.97
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 P20671
- Every structure of UniProt Q96A08
- Elsewhere: RCSB PDB 5GT3 · PDBe 5GT3 · UniProt P68431 · UniProt P62805 · UniProt P20671 · UniProt Q96A08
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