Research workbench
Chromatin remodeller-nucleosome complex at 4.5 a resolution.
Analyse Chromatin remodeller-nucleosome complex at 4.5 a resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GEN
- Type
- protein + DNA
- Length
- 5,160 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 72; Histone H3; Histone H4; Histone H2A.1…
- EC
- 3.6.4.12
- UniProt
- P61830, P02309, P04911, P02293, Q05471, Q12509, Q03433, Q03940, Q12464
- Ligands
- ADP, BEF, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 19 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Vacuolar protein sorting-associated protein 72 | protein | 131 | 24% helix, 5% strand | — |
| A, B | Histone H3 | protein | 97 | 55% helix, 4% strand | P61830 |
| C | Histone H4 | protein | 82 | 56% helix, 5% strand | P02309 |
| D | Histone H4 | protein | 80 | 58% helix, 6% strand | P02309 |
| E | Histone H2A.1 | protein | 103 | 52% helix, 4% strand | P04911 |
| F | Histone H2A.1 | protein | 101 | 53% helix, 5% strand | P04911 |
| G | Histone H2B.1 | protein | 96 | 72% helix, 4% strand | P02293 |
| H | Histone H2B.1 | protein | 91 | 75% helix, 4% strand | P02293 |
| I | DNA (173-mer) | dna | 173 | — | — |
| J | DNA (173-mer) | dna | 173 | — | — |
| M | Helicase SWR1 (EC 3.6.4.12) | protein | 688 | 42% helix, 8% strand | Q05471 |
| R | Actin-like protein ARP6 | protein | 411 | 33% helix, 18% strand | Q12509 |
| S | Vacuolar protein sorting-associated protein 71 | protein | 208 | 38% helix, 2% strand | Q03433 |
| T | Ruvb-like protein 1 (EC 3.6.4.12) | protein | 443 | 38% helix, 21% strand | Q03940 |
| U | Ruvb-like protein 2 (EC 3.6.4.12) | protein | 430 | 38% helix, 22% strand | Q12464 |
| V | Ruvb-like protein 1 (EC 3.6.4.12) | protein | 434 | 39% helix, 22% strand | Q03940 |
| W | Ruvb-like protein 2 (EC 3.6.4.12) | protein | 433 | 37% helix, 21% strand | Q12464 |
| X | Ruvb-like protein 1 (EC 3.6.4.12) | protein | 442 | 38% helix, 21% strand | Q03940 |
| Y | Ruvb-like protein 2 (EC 3.6.4.12) | protein | 447 | 36% helix, 20% strand | Q12464 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains M, R, T, U, V, W, X, Y
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains M, R
- MG · Magnesium ion · metal · 8 copies · chains M, R, T, U, V, W, X, Y
- ZN · Zinc ion · metal · 2 copies · chains S
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 | 1025 | 0.88 | 0.89 | 108 | empty |
| 2 | 775 | 0.87 | 0.90 | 103 | ADP, MG |
| 3 | 971 | 0.87 | 0.88 | 113 | ADP, MG |
| 4 | 1088 | 0.87 | 0.88 | 115 | ADP, MG |
| 5 | 1007 | 0.85 | 0.86 | 83 | empty |
Interfaces
70 interfaces between chains.
- I–J · 8180 Ų buried · 674 hydrogen bonds · nucleic-nucleic
- R–S · 3906 Ų buried · 31 hydrogen bonds · protein-protein
- T–U · 3066 Ų buried · 21 hydrogen bonds · protein-protein
- U–V · 2988 Ų buried · 12 hydrogen bonds · protein-protein
- V–W · 2704 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6GEN · Chromatin remodeller-nucleosome complex at 4.5 A resolution. · the same entry in another collection · chain J against J, 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 P61830
- Every structure of UniProt P02309
- Every structure of UniProt P04911
- Every structure of UniProt P02293
- Every structure of UniProt Q05471
- Every structure of UniProt Q12509
- Every structure of UniProt Q03433
- Every structure of UniProt Q03940
- Every structure of UniProt Q12464
- Elsewhere: RCSB PDB 6GEN · PDBe 6GEN · UniProt P61830 · UniProt P02309 · UniProt P04911 · UniProt P02293 · UniProt Q05471 · UniProt Q12509 · UniProt Q03433 · UniProt Q03940 · UniProt Q12464
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