MolNFT v1 · #185553 · protein + DNA + RNA
RNA polymerase elongation complex in less-swiveled conformation
7Q0K · Ntdna: “RNA polymerase elongation complex in less-swiveled conformation”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #185553 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7Q0K
- Type
- protein + DNA + RNA
- Length
- 3,253 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ntdna; Tdna; RNA; DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V4, P0A8T8, P0A800
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Ntdna | dna | 24 | — | — |
| T | Tdna | dna | 34 | — | — |
| R | RNA | rna | 11 | — | — |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 22% helix, 35% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 19% helix, 37% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1337 | 29% helix, 21% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 37% helix, 16% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 73 | 60% helix, 0% strand | P0A800 |
Ligands and binding sites
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 | 1075 | 0.84 | 0.85 | 108 | empty |
| 2 | 431 | 0.81 | 0.89 | 51 | empty |
| 3 | 430 | 0.79 | 0.88 | 63 | empty |
| 4 | 666 | 0.79 | 0.84 | 61 | empty |
| 5 | 620 | 0.78 | 0.84 | 55 | empty |
Interfaces
15 interfaces between chains.
- C–D · 7972 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 1940 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1805 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1273 Ų buried · 10 hydrogen bonds · protein-protein
- N–T · 1051 Ų buried · 78 hydrogen bonds · nucleic-nucleic
Compared structures
- 7Q0K · RNA polymerase elongation complex in less-swiveled conformation · the same entry in another collection · chain B against B, TM-score 1.00
- P0A8T8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T8) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 P0A7Z4
- Every structure of UniProt P0A8V4
- Every structure of UniProt P0A8T8
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 7Q0K · PDBe 7Q0K · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T8 · UniProt P0A800
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