Research workbench
RNA polymerase I pre-initiation complex DNA opening intermediate 1
Analyse RNA polymerase I pre-initiation complex DNA opening intermediate 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RRD
- Type
- protein + DNA
- Length
- 6,278 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Template strand; Nontemplate strand; RNA polymerase I-specific transcription initiation…
- EC
- 2.7.7.6
- UniProt
- P40992, P32786, Q04712, P32529, P47006, Q01080, P10964, P22138, P07703, P50106, P20434, P20435, P46669, P20436, P22139, P28000, P40422, P36070
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 20 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Template strand | dna | 51 | — | — |
| U | Nontemplate strand | dna | 48 | — | — |
| Q | RNA polymerase I-specific transcription initiation factor RRN7 | protein | 477 | 40% helix, 2% strand | P40992 |
| S | RNA polymerase I-specific transcription initiation factor RRN6 | protein | 610 | 15% helix, 23% strand | P32786 |
| R | RNA polymerase I-specific transcription initiation factor RRN11 | protein | 330 | 52% helix, 1% strand | Q04712 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 124 | 4% helix, 22% strand | P32529 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 139 | 0% helix, 24% strand | P47006 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 108 | 6% helix, 44% strand | Q01080 |
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1465 | 39% helix, 12% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1180 | 25% helix, 25% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 304 | 22% helix, 29% strand | P07703 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 70 | 41% helix, 7% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 215 | 37% 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 | 12% helix, 35% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 134 | 3% helix, 51% 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 | 38% helix, 23% 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 |
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 | 1078 | 0.85 | 0.87 | 86 | empty |
| 2 | 1122 | 0.85 | 0.86 | 130 | empty |
| 3 | 628 | 0.85 | 0.90 | 74 | empty |
| 4 | 1118 | 0.83 | 0.85 | 93 | empty |
| 5 | 1093 | 0.83 | 0.84 | 125 | empty |
Interfaces
56 interfaces between chains.
- A–B · 9052 Ų buried · 118 hydrogen bonds · protein-protein
- S–R · 4235 Ų buried · 44 hydrogen bonds · protein-protein
- Q–S · 4136 Ų buried · 28 hydrogen bonds · protein-protein
- I–A · 2951 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 2879 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6RRD · RNA Polymerase I Pre-initiation complex DNA opening intermediate 1 · the same entry in another collection · chain S against S, 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 P40992
- Every structure of UniProt P32786
- Every structure of UniProt Q04712
- 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
- Elsewhere: RCSB PDB 6RRD · PDBe 6RRD · UniProt P40992 · UniProt P32786 · UniProt Q04712 · 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
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