Research workbench
Cryo-EM structure of the nucleosome containing giardia histones
Analyse Cryo-EM structure of the nucleosome containing giardia histones in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D69
- Type
- protein + DNA
- Length
- 977 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2B; Histone H2A; 601L DNA (145-mer)
- UniProt
- V6TEE9, E2RU60, V6TJV6, E2RU15
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 7 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 90 | 62% helix, 4% strand | V6TEE9 |
| B, F | Histone H4 | protein | 78 | 64% helix, 8% strand | E2RU60 |
| D, H | Histone H2B | protein | 96 | 75% helix, 2% strand | V6TJV6 |
| E | Histone H3 | protein | 99 | 64% helix, 4% strand | V6TEE9 |
| C, G | Histone H2A | protein | 95 | 58% helix, 5% strand | E2RU15 |
| I | 601L DNA (145-mer) | dna | 125 | — | — |
| J | 601L DNA (145-mer) | dna | 125 | — | — |
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 | 682 | 0.78 | 0.83 | 68 | empty |
| 2 | 210 | 0.64 | 0.84 | 28 | empty |
| 3 | 225 | 0.64 | 0.83 | 36 | empty |
| 4 | 376 | 0.60 | 0.77 | 29 | empty |
| 5 | 427 | 0.60 | 0.76 | 27 | empty |
Interfaces
35 interfaces between chains.
- I–J · 5547 Ų buried · 471 hydrogen bonds · nucleic-nucleic
- D–C · 2753 Ų buried · 20 hydrogen bonds · protein-protein
- H–G · 2692 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2669 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2571 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7D69 · Cryo-EM structure of the nucleosome containing Giardia histones · the same entry in another collection · chain F against F, 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 V6TEE9
- Every structure of UniProt E2RU60
- Every structure of UniProt V6TJV6
- Every structure of UniProt E2RU15
- Elsewhere: RCSB PDB 7D69 · PDBe 7D69 · UniProt V6TEE9 · UniProt E2RU60 · UniProt V6TJV6 · UniProt E2RU15
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