MolNFT v1 · #154558 · protein + DNA
Cryo-EM structure of thermococcus kodakarensis RNA polymerase
6KF9 · 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 #154558 on GenesisL1: 3D structure…
- PDB
- 6KF9
- Type
- protein + DNA
- Length
- 3,486 residues
- Chains
- 14
- 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, Q5JDD5
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 14 distinct chains · 30% 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 | 32% 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 | 12% helix, 44% strand | Q5JIY4 |
| F | DNA-directed RNA polymerase, subunit F | protein | 122 | 57% helix, 7% 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 | 38% helix, 5% 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, 27% strand | Q5JDM8 |
| G | Transcription factor E | protein | 166 | 57% helix, 12% strand | Q5JDD5 |
| X | DNA (5'- D(P*TP*CP*GP*GP*TP*AP*AP*TP*CP*AP*CP*GP*CP*TP*CP*C)-3') | dna | 14 | — | — |
| Y | DNA (27-mer) | dna | 9 | — | — |
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 | 827 | 0.84 | 0.87 | 106 | empty |
| 2 | 584 | 0.79 | 0.85 | 77 | empty |
| 3 | 984 | 0.79 | 0.81 | 86 | empty |
| 4 | 1001 | 0.79 | 0.80 | 106 | empty |
| 5 | 523 | 0.77 | 0.85 | 42 | empty |
Interfaces
34 interfaces between chains.
- A–B · 9035 Ų buried · 84 hydrogen bonds · protein-protein
- A–C · 5116 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2243 Ų buried · 18 hydrogen bonds · protein-protein
- D–L · 1710 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1631 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6KF9 · Cryo-EM structure of Thermococcus kodakarensis RNA polymerase · the same entry in another collection · chain Y against Y, 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 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
- Every structure of UniProt Q5JDD5
- Elsewhere: RCSB PDB 6KF9 · PDBe 6KF9 · UniProt Q5JE33 · UniProt Q5JE32 · UniProt Q5JE34 · UniProt Q5JJF4 · UniProt Q5JIY4 · UniProt Q5JI52 · UniProt Q5JE31 · UniProt Q5JJD0 · UniProt Q5JE88 · UniProt Q5JJC9 · UniProt Q5JDM8 · UniProt Q5JDD5
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