Research workbench
RNA polymerase-GP39 complex
Analyse RNA polymerase-GP39 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WOD
- Type
- protein
- Length
- 3,654 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1, A7XX65
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 20% helix, 40% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 232 | 20% helix, 41% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1118 | 25% helix, 23% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1488 | 34% helix, 16% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 95 | 45% helix, 4% strand | Q8RQE7 |
| F | RNA polymerase sigma factor | protein | 278 | 65% helix, 1% strand | Q5SKW1 |
| G | Putative uncharacterized protein | protein | 127 | 15% helix, 34% strand | A7XX65 |
| H | Putative uncharacterized protein | protein | 91 | 9% helix, 33% strand | A7XX65 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains D
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 | 1077 | 0.86 | 0.87 | 106 | empty |
| 2 | 787 | 0.86 | 0.89 | 88 | empty |
| 3 | 432 | 0.82 | 0.89 | 53 | empty |
| 4 | 976 | 0.81 | 0.83 | 97 | empty |
| 5 | 266 | 0.81 | 0.93 | 50 | empty |
Interfaces
16 interfaces between chains.
- C–D · 8718 Ų buried · 95 hydrogen bonds · protein-protein
- D–F · 3279 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 2422 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 2238 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1804 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3WOD · RNA polymerase-gp39 complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q8RQE9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q8RQE9) · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q8RQE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q8RQE7) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Every structure of UniProt A7XX65
- Elsewhere: RCSB PDB 3WOD · PDBe 3WOD · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1 · UniProt A7XX65
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