MolNFT v1 · #149927 · protein + DNA
Chromatin remodeller-nucleosome complex at 3.6 a resolution.
6GEJ · Vacuolar protein sorting-associated protein 72: “Chromatin remodeller-nucleosome complex at 3.6 a resolution.”. Electron microscopy, 4 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.88). MolNFT v1 #149927 on GenesisL1: 3D…
- PDB
- 6GEJ
- Type
- protein + DNA
- Length
- 5,122 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 · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Vacuolar protein sorting-associated protein 72 | protein | 131 | 32% helix, 8% strand | — |
| A, B | Histone H3 | protein | 97 | 60% helix, 4% strand | P61830 |
| C | Histone H4 | protein | 82 | 59% helix, 6% strand | P02309 |
| D | Histone H4 | protein | 80 | 60% helix, 6% strand | P02309 |
| E | Histone H2A.1 | protein | 103 | 54% helix, 5% strand | P04911 |
| F | Histone H2A.1 | protein | 101 | 55% 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 (154-mer) | dna | 154 | — | — |
| J | DNA (154-mer) | dna | 154 | — | — |
| M | Helicase SWR1 (EC 3.6.4.12) | protein | 688 | 44% helix, 8% strand | Q05471 |
| R | Actin-like protein ARP6 | protein | 411 | 36% helix, 19% strand | Q12509 |
| S | Vacuolar protein sorting-associated protein 71 | protein | 208 | 40% helix, 4% strand | Q03433 |
| T | Ruvb-like protein 1 (EC 3.6.4.12) | protein | 443 | 40% helix, 23% strand | Q03940 |
| U | Ruvb-like protein 2 (EC 3.6.4.12) | protein | 430 | 39% helix, 23% strand | Q12464 |
| V | Ruvb-like protein 1 (EC 3.6.4.12) | protein | 434 | 39% helix, 21% strand | Q03940 |
| W | Ruvb-like protein 2 (EC 3.6.4.12) | protein | 433 | 38% helix, 23% strand | Q12464 |
| X | Ruvb-like protein 1 (EC 3.6.4.12) | protein | 442 | 38% helix, 25% strand | Q03940 |
| Y | Ruvb-like protein 2 (EC 3.6.4.12) | protein | 447 | 36% helix, 22% 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 | 1143 | 0.88 | 0.89 | 137 | empty |
| 2 | 418 | 0.86 | 0.94 | 61 | ADP, MG |
| 3 | 342 | 0.85 | 0.94 | 41 | ADP, MG |
| 4 | 914 | 0.84 | 0.86 | 67 | empty |
| 5 | 333 | 0.84 | 0.94 | 42 | ADP |
Interfaces
73 interfaces between chains.
- I–J · 7108 Ų buried · 595 hydrogen bonds · nucleic-nucleic
- T–Y · 3918 Ų buried · 28 hydrogen bonds · protein-protein
- R–S · 3852 Ų buried · 31 hydrogen bonds · protein-protein
- U–V · 3495 Ų buried · 25 hydrogen bonds · protein-protein
- W–X · 3477 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6GEJ · Chromatin remodeller-nucleosome complex at 3.6 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 6GEJ · PDBe 6GEJ · UniProt P61830 · UniProt P02309 · UniProt P04911 · UniProt P02293 · UniProt Q05471 · UniProt Q12509 · UniProt Q03433 · UniProt Q03940 · UniProt Q12464
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