MolNFT v1 · #154553 · protein
Cryo-EM structure of thermococcus kodakarensis RNA polymerase
6KF3 · DNA-directed RNA polymerase subunit: “Cryo-EM structure of thermococcus kodakarensis RNA polymerase”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #154553 on GenesisL1: 3D structure…
- PDB
- 6KF3
- Type
- protein
- Length
- 3,297 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q5JE33, Q5JE32, Q5JE34, Q5JJF4, Q5JIY4, Q5JI52, Q5JE31, Q5JJD0, Q5JE88, Q5JJC9, Q5JDM8
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 11 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 900 | 33% helix, 12% strand | Q5JE33 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1114 | 25% helix, 19% strand | Q5JE32 |
| C | DNA-directed RNA polymerase subunit a'' (EC 2.7.7.6) | protein | 388 | 34% helix, 6% strand | Q5JE34 |
| D | DNA-directed RNA polymerase subunit D (EC 2.7.7.6) | protein | 257 | 26% helix, 39% strand | Q5JJF4 |
| E | DNA-directed RNA polymerase, subunit E | protein | 181 | 10% helix, 45% strand | Q5JIY4 |
| F | DNA-directed RNA polymerase, subunit F | protein | 122 | 54% helix, 6% strand | Q5JI52 |
| H | DNA-directed RNA polymerase subunit H (EC 2.7.7.6) | protein | 76 | 13% helix, 30% strand | Q5JE31 |
| K | DNA-directed RNA polymerase subunit K (EC 2.7.7.6) | protein | 56 | 43% helix, 4% strand | Q5JJD0 |
| L | DNA-directed RNA polymerase subunit L (EC 2.7.7.6) | protein | 94 | 38% helix, 27% strand | Q5JE88 |
| N | DNA-directed RNA polymerase subunit N (EC 2.7.7.6) | protein | 65 | 35% helix, 0% strand | Q5JJC9 |
| P | DNA-directed RNA polymerase subunit P (EC 2.7.7.6) | protein | 44 | 0% helix, 25% strand | Q5JDM8 |
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 | 1199 | 0.84 | 0.85 | 149 | empty |
| 2 | 166 | 0.78 | 0.94 | 44 | empty |
| 3 | 550 | 0.77 | 0.84 | 64 | empty |
| 4 | 971 | 0.76 | 0.79 | 94 | empty |
| 5 | 407 | 0.75 | 0.85 | 50 | empty |
Interfaces
24 interfaces between chains.
- A–B · 8800 Ų buried · 83 hydrogen bonds · protein-protein
- A–C · 5063 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2136 Ų buried · 15 hydrogen bonds · protein-protein
- D–L · 1698 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1613 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6KF3 · Cryo-EM structure of Thermococcus kodakarensis RNA polymerase · the same entry in another collection · chain P against P, TM-score 1.00
- Q5JJF4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit D (Q5JJF4) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q5JE33
- Every structure of UniProt Q5JE32
- Every structure of UniProt Q5JE34
- Every structure of UniProt Q5JJF4
- Every structure of UniProt Q5JIY4
- Every structure of UniProt Q5JI52
- Every structure of UniProt Q5JE31
- Every structure of UniProt Q5JJD0
- Every structure of UniProt Q5JE88
- Every structure of UniProt Q5JJC9
- Every structure of UniProt Q5JDM8
- Elsewhere: RCSB PDB 6KF3 · PDBe 6KF3 · UniProt Q5JE33 · UniProt Q5JE32 · UniProt Q5JE34 · UniProt Q5JJF4 · UniProt Q5JIY4 · UniProt Q5JI52 · UniProt Q5JE31 · UniProt Q5JJD0 · UniProt Q5JE88 · UniProt Q5JJC9 · UniProt Q5JDM8
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