MolNFT v1 · #163162 · protein + DNA
RNA polymerase I pre-initiation complex DNA opening intermediate 2
6RUI · Template strand: “RNA polymerase I pre-initiation complex DNA opening intermediate 2”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #163162 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6RUI
- Type
- protein + DNA
- Length
- 6,273 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Template strand; Nontemplate strand; DNA-directed RNA polymerase I subunit RPA12…
- EC
- 2.7.7.6
- UniProt
- P32529, P47006, Q01080, P10964, P22138, P07703, P50106, P20434, P20435, P46669, P20436, P22139, P28000, P40422, P36070, P40992, P32786, Q04712
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 20 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Template strand | dna | 48 | — | — |
| U | Nontemplate strand | dna | 46 | — | — |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 124 | 3% helix, 16% strand | P32529 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 139 | 5% helix, 24% strand | P47006 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 108 | 4% helix, 46% strand | Q01080 |
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1465 | 40% helix, 13% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1180 | 26% helix, 26% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 304 | 23% helix, 29% strand | P07703 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 70 | 34% helix, 7% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 215 | 36% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 100 | 39% helix, 14% strand | P20435 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 202 | 10% helix, 39% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 134 | 2% helix, 50% strand | P20436 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 41% helix, 4% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 103 | 37% helix, 24% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 29% strand | P40422 |
| O | RNA polymerase I-specific transcription initiation factor RRN3 | protein | 504 | 54% helix, 0% strand | P36070 |
| Q | RNA polymerase I-specific transcription initiation factor RRN7 | protein | 477 | 45% helix, 3% strand | P40992 |
| S | RNA polymerase I-specific transcription initiation factor RRN6 | protein | 610 | 17% helix, 25% strand | P32786 |
| R | RNA polymerase I-specific transcription initiation factor RRN11 | protein | 330 | 56% helix, 2% strand | Q04712 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains Q
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 | 929 | 0.86 | 0.88 | 83 | empty |
| 2 | 888 | 0.85 | 0.87 | 112 | empty |
| 3 | 1081 | 0.83 | 0.84 | 104 | empty |
| 4 | 996 | 0.83 | 0.84 | 128 | empty |
| 5 | 707 | 0.83 | 0.87 | 94 | empty |
Interfaces
55 interfaces between chains.
- A–B · 9125 Ų buried · 116 hydrogen bonds · protein-protein
- S–R · 4275 Ų buried · 41 hydrogen bonds · protein-protein
- Q–S · 4116 Ų buried · 21 hydrogen bonds · protein-protein
- I–A · 2904 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 2881 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6RUI · RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 · the same entry in another collection · chain B against B, 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 P32529
- Every structure of UniProt P47006
- Every structure of UniProt Q01080
- Every structure of UniProt P10964
- Every structure of UniProt P22138
- Every structure of UniProt P07703
- Every structure of UniProt P50106
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P46669
- Every structure of UniProt P20436
- Every structure of UniProt P22139
- Every structure of UniProt P28000
- Every structure of UniProt P40422
- Every structure of UniProt P36070
- Every structure of UniProt P40992
- Every structure of UniProt P32786
- Every structure of UniProt Q04712
- Elsewhere: RCSB PDB 6RUI · PDBe 6RUI · UniProt P32529 · UniProt P47006 · UniProt Q01080 · UniProt P10964 · UniProt P22138 · UniProt P07703 · UniProt P50106 · UniProt P20434 · UniProt P20435 · UniProt P46669 · UniProt P20436 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt P36070 · UniProt P40992 · UniProt P32786 · UniProt Q04712
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