Research workbench
RNA polymerase I elongation complex 2
Analyse RNA polymerase I elongation complex 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M5Y
- Type
- protein + DNA + RNA
- Length
- 4,212 residues
- Chains
- 17
- 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 0.84
Structure
electron microscopy · 17 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1466 | 40% helix, 10% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1170 | 24% helix, 21% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 304 | 21% helix, 28% strand | P07703 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 59 | 46% helix, 8% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 39% helix, 24% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 100 | 43% helix, 11% strand | P20435 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 202 | 10% helix, 38% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 134 | 5% helix, 43% strand | P20436 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 64 | 6% helix, 22% strand | P32529 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 38% helix, 0% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 100 | 38% helix, 25% 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 | 101 | 0% helix, 36% strand | Q01080 |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 135 | 0% helix, 19% strand | P47006 |
| R | RNA | rna | 7 | — | — |
| S | Non-template DNA | dna | 19 | — | — |
| T | Template DNA | dna | 25 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 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 | 822 | 0.84 | 0.86 | 105 | empty |
| 2 | 790 | 0.82 | 0.85 | 117 | empty |
| 3 | 1007 | 0.81 | 0.82 | 109 | empty |
| 4 | 509 | 0.81 | 0.88 | 58 | empty |
| 5 | 246 | 0.80 | 0.93 | 35 | empty |
Interfaces
40 interfaces between chains.
- A–B · 9263 Ų buried · 91 hydrogen bonds · protein-protein
- A–E · 2912 Ų buried · 45 hydrogen bonds · protein-protein
- M–N · 2281 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 2126 Ų buried · 20 hydrogen bonds · protein-protein
- B–J · 2020 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5M5Y · RNA Polymerase I elongation complex 2 · 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 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 5M5Y · PDBe 5M5Y · 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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