Research workbench
Cryo-EM structure of thermococcus kodakarensis RNA polymerase
Analyse Cryo-EM structure of thermococcus kodakarensis RNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KF4
- Type
- protein
- Length
- 3,462 residues
- Chains
- 12
- 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 0.81
Structure
electron microscopy · 12 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 901 | 34% helix, 13% strand | Q5JE33 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1114 | 30% helix, 21% strand | Q5JE32 |
| C | DNA-directed RNA polymerase subunit a'' (EC 2.7.7.6) | protein | 388 | 34% helix, 7% strand | Q5JE34 |
| D | DNA-directed RNA polymerase subunit D (EC 2.7.7.6) | protein | 257 | 26% helix, 38% strand | Q5JJF4 |
| E | DNA-directed RNA polymerase, subunit E | protein | 181 | 16% helix, 48% strand | Q5JIY4 |
| F | DNA-directed RNA polymerase, subunit F | protein | 122 | 54% helix, 7% strand | Q5JI52 |
| H | DNA-directed RNA polymerase subunit H (EC 2.7.7.6) | protein | 76 | 22% helix, 28% strand | Q5JE31 |
| K | DNA-directed RNA polymerase subunit K (EC 2.7.7.6) | protein | 56 | 46% helix, 4% strand | Q5JJD0 |
| L | DNA-directed RNA polymerase subunit L (EC 2.7.7.6) | protein | 94 | 37% helix, 22% strand | Q5JE88 |
| N | DNA-directed RNA polymerase subunit N (EC 2.7.7.6) | protein | 65 | 46% helix, 0% strand | Q5JJC9 |
| P | DNA-directed RNA polymerase subunit P (EC 2.7.7.6) | protein | 42 | 0% helix, 17% strand | Q5JDM8 |
| G | Transcription factor E | protein | 166 | 55% helix, 11% strand | Q5JDD5 |
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 | 608 | 0.81 | 0.86 | 79 | empty |
| 2 | 567 | 0.80 | 0.86 | 83 | empty |
| 3 | 794 | 0.79 | 0.82 | 77 | empty |
| 4 | 593 | 0.77 | 0.84 | 88 | empty |
| 5 | 886 | 0.77 | 0.80 | 91 | empty |
Interfaces
27 interfaces between chains.
- A–B · 8426 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 4905 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2295 Ų buried · 15 hydrogen bonds · protein-protein
- D–L · 1692 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1569 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6KF4 · Cryo-EM structure of Thermococcus kodakarensis RNA polymerase · the same entry in another collection · chain G against G, 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 6KF4 · PDBe 6KF4 · 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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