MolNFT v1 · #167898 · protein + DNA
Cryo-EM structure of STH1-ARP7-ARP9-RTT102 bound to the nucleosome in ADP beryllium fluoride state
6VZ4 · Histone H3: “Cryo-EM structure of STH1-ARP7-ARP9-RTT102 bound to the nucleosome in ADP beryllium fluoride state”. Electron microscopy, 4 ligands (ADP, BEF, ATP), 20 pockets (best druggability 0.83). MolNFT v1 #167898 on GenesisL1…
- PDB
- 6VZ4
- Type
- protein + DNA
- Length
- 2,509 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (185-mer); Nuclear protein…
- EC
- 3.6.4.12
- UniProt
- Q92133, P62799, Q6AZJ8, Q92130, P32597, Q12406, Q05123, P53330
- Ligands
- ADP, BEF, ATP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 12 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 98 | 65% helix, 4% strand | Q92133 |
| B | Histone H4 | protein | 87 | 57% helix, 8% strand | P62799 |
| C, G | Histone H2A | protein | 107 | 53% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B | protein | 92 | 74% helix, 4% strand | Q92130 |
| E | Histone H3 | protein | 95 | 66% helix, 4% strand | Q92133 |
| F | Histone H4 | protein | 79 | 59% helix, 9% strand | P62799 |
| I | DNA (185-mer) | dna | 146 | — | — |
| J | DNA (185-mer) | dna | 146 | — | — |
| K | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 616 | 56% helix, 9% strand | P32597 |
| L | Actin-related protein 7 | protein | 393 | 46% helix, 19% strand | Q12406 |
| M | Actin-like protein ARP9 | protein | 396 | 42% helix, 19% strand | Q05123 |
| N | Regulator of TY1 transposition protein 102 | protein | 55 | 13% helix, 27% strand | P53330 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains K
- BEF · Beryllium trifluoride ion · ligand · chains K
- ATP · Adenosine-5'-triphosphate · ligand · chains L
- MG · Magnesium ion · metal · chains K
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 | 1133 | 0.83 | 0.84 | 120 | ATP |
| 2 | 290 | 0.82 | 0.94 | 28 | empty |
| 3 | 473 | 0.81 | 0.88 | 54 | empty |
| 4 | 1081 | 0.79 | 0.80 | 84 | empty |
| 5 | 529 | 0.76 | 0.83 | 54 | empty |
Interfaces
43 interfaces between chains.
- I–J · 6551 Ų buried · 474 hydrogen bonds · nucleic-nucleic
- G–H · 2514 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2495 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2448 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2437 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6VZ4 · Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium… · the same entry in another collection · chain N against N, 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 Q92133
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt Q92130
- Every structure of UniProt P32597
- Every structure of UniProt Q12406
- Every structure of UniProt Q05123
- Every structure of UniProt P53330
- Elsewhere: RCSB PDB 6VZ4 · PDBe 6VZ4 · UniProt Q92133 · UniProt P62799 · UniProt Q6AZJ8 · UniProt Q92130 · UniProt P32597 · UniProt Q12406 · UniProt Q05123 · UniProt P53330
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