MolNFT v1 · #184032 · protein + DNA + RNA
Cryo-EM structure of human RNA polymerase I in elongation state
7OB9 · DNA-directed RNA polymerase I subunit RPA1: “Cryo-EM structure of human RNA polymerase I in elongation state”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #184032 on GenesisL1: 3D…
- PDB
- 7OB9
- Type
- protein + DNA + RNA
- Length
- 4,466 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase I subunit RPA1; DNA-directed RNA polymerase I subunit RPA2…
- EC
- 2.7.7.6
- UniProt
- O95602, Q9H9Y6, O15160, P19388, P61218, Q3B726, P52434, Q9P1U0, P62875, P0DPB6, P53803, O15446, Q9GZS1
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 16 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA1 (EC 2.7.7.6) | protein | 1535 | 41% helix, 13% strand | O95602 |
| B | DNA-directed RNA polymerase I subunit RPA2 (EC 2.7.7.6) | protein | 1129 | 25% helix, 24% strand | Q9H9Y6 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 307 | 29% helix, 33% strand | O15160 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 209 | 35% helix, 21% strand | P19388 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 79 | 37% helix, 11% strand | P61218 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 176 | 12% helix, 38% strand | Q3B726 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 149 | 2% helix, 44% strand | P52434 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 55 | 11% helix, 25% strand | Q9P1U0 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 67 | 46% helix, 4% strand | P62875 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 107 | 43% helix, 26% strand | P0DPB6 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 47 | 0% helix, 32% strand | P53803 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 149 | 0% helix, 25% strand | O15446 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 388 | 29% helix, 17% strand | Q9GZS1 |
| R | RNA | rna | 21 | — | — |
| S | DNA non-template strand | dna | 19 | — | — |
| T | DNA template strand | dna | 29 | — | — |
Ligands and binding sites
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 | 592 | 0.84 | 0.90 | 66 | empty |
| 2 | 1005 | 0.83 | 0.85 | 120 | empty |
| 3 | 1151 | 0.83 | 0.84 | 104 | empty |
| 4 | 972 | 0.82 | 0.84 | 88 | empty |
| 5 | 406 | 0.82 | 0.91 | 41 | empty |
Interfaces
42 interfaces between chains.
- A–B · 9197 Ų buried · 94 hydrogen bonds · protein-protein
- A–E · 3632 Ų buried · 57 hydrogen bonds · protein-protein
- N–M · 2539 Ų buried · 47 hydrogen bonds · protein-protein
- A–H · 2192 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 2067 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7OB9 · Cryo-EM structure of human RNA Polymerase I in elongation state · the same entry in another collection · chain K against K, 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 O95602
- Every structure of UniProt Q9H9Y6
- Every structure of UniProt O15160
- Every structure of UniProt P19388
- Every structure of UniProt P61218
- Every structure of UniProt Q3B726
- Every structure of UniProt P52434
- Every structure of UniProt Q9P1U0
- Every structure of UniProt P62875
- Every structure of UniProt P0DPB6
- Every structure of UniProt P53803
- Every structure of UniProt O15446
- Every structure of UniProt Q9GZS1
- Elsewhere: RCSB PDB 7OB9 · PDBe 7OB9 · UniProt O95602 · UniProt Q9H9Y6 · UniProt O15160 · UniProt P19388 · UniProt P61218 · UniProt Q3B726 · UniProt P52434 · UniProt Q9P1U0 · UniProt P62875 · UniProt P0DPB6 · UniProt P53803 · UniProt O15446 · UniProt Q9GZS1
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