MolNFT v1 · #126538 · protein + DNA
RNA polymerase I open complex
5M5W · DNA-directed RNA polymerase I subunit RPA190: “RNA polymerase I open complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #126538 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M5W
- Type
- protein + DNA
- Length
- 4,314 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase I subunit RPA190; DNA-directed RNA polymerase I subunit…
- EC
- 2.7.7.6
- UniProt
- P10964, P22138, P07703, P50106, P20434, P20435, P46669, P20436, P32529, P22139, P28000, P40422, Q01080, P47006
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 16 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1493 | 39% helix, 12% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1183 | 24% helix, 21% 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 | 59 | 37% helix, 8% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 36% helix, 21% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 100 | 45% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 205 | 10% helix, 41% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 134 | 2% helix, 49% strand | P20436 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 114 | 4% helix, 20% strand | P32529 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 39% helix, 1% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 100 | 40% helix, 26% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 43 | 0% helix, 28% strand | P40422 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 107 | 0% helix, 34% strand | Q01080 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 146 | 3% helix, 23% strand | P47006 |
| S | Non-template strand | dna | 18 | — | — |
| T | Template strand | dna | 25 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, I, M, J, L
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 | 1111 | 0.86 | 0.87 | 111 | empty |
| 2 | 340 | 0.81 | 0.91 | 40 | empty |
| 3 | 1049 | 0.81 | 0.82 | 102 | empty |
| 4 | 977 | 0.81 | 0.82 | 93 | empty |
| 5 | 1031 | 0.80 | 0.82 | 100 | empty |
Interfaces
38 interfaces between chains.
- A–B · 9833 Ų buried · 116 hydrogen bonds · protein-protein
- A–E · 2867 Ų buried · 41 hydrogen bonds · protein-protein
- A–I · 2656 Ų buried · 35 hydrogen bonds · protein-protein
- M–N · 2421 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2233 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5M5W · RNA Polymerase I open complex · the same entry in another collection · chain I against I, 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 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 P32529
- Every structure of UniProt P22139
- Every structure of UniProt P28000
- Every structure of UniProt P40422
- Every structure of UniProt Q01080
- Every structure of UniProt P47006
- Elsewhere: RCSB PDB 5M5W · PDBe 5M5W · UniProt P10964 · UniProt P22138 · UniProt P07703 · UniProt P50106 · UniProt P20434 · UniProt P20435 · UniProt P46669 · UniProt P20436 · UniProt P32529 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt Q01080 · UniProt P47006
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