MolNFT v1 · #125903 · protein
Monomeric RNA polymerase I at 4.9 a resolution
5LMX · DNA-directed RNA polymerase I subunit RPA190: “Monomeric RNA polymerase I at 4.9 a resolution”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #125903 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LMX
- Type
- protein
- Length
- 3,918 residues
- Chains
- 14
- 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 · 14 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1420 | 44% helix, 13% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1115 | 29% helix, 26% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1,DNA- directed RNA polymerases I and III subunit RPAC1 | protein | 304 | 24% helix, 33% strand | P07703 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 18 | 0% helix, 22% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 215 | 40% helix, 24% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 100 | 42% helix, 13% strand | P20435 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 89 | 15% helix, 45% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 134 | 5% helix, 50% strand | P20436 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 64 | 8% helix, 20% strand | P32529 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 41% helix, 0% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 101 | 41% helix, 25% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 27% strand | P40422 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 105 | 4% helix, 50% strand | Q01080 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 139 | 3% helix, 27% strand | P47006 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, I, 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 | 867 | 0.86 | 0.88 | 132 | empty |
| 2 | 977 | 0.84 | 0.85 | 130 | empty |
| 3 | 540 | 0.84 | 0.90 | 83 | empty |
| 4 | 889 | 0.82 | 0.84 | 98 | empty |
| 5 | 889 | 0.82 | 0.84 | 97 | empty |
Interfaces
31 interfaces between chains.
- A–B · 6383 Ų buried · 71 hydrogen bonds · protein-protein
- M–N · 2465 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 1938 Ų buried · 10 hydrogen bonds · protein-protein
- C–K · 1892 Ų buried · 10 hydrogen bonds · protein-protein
- B–J · 1566 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5LMX · Monomeric RNA polymerase I at 4.9 A resolution · 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 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 5LMX · PDBe 5LMX · 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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