Research workbench
Mfd-bound E.COLI RNA polymerase elongation complex - IV state
Analyse Mfd-bound E.COLI RNA polymerase elongation complex - IV state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X4Y
- Type
- protein + DNA + RNA
- Length
- 4,429 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription-repair-coupling factor; DNA-directed RNA polymerase subunit alpha…
- EC
- 3.6.4.-, 2.7.7.6
- UniProt
- A0A024L3Y3, A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
- Ligands
- ADP, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription-repair-coupling factor (EC 3.6.4.-) | protein | 1144 | 35% helix, 16% strand | A0A024L3Y3 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 19% helix, 37% strand | A0A073G207 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 18% helix, 32% strand | A0A073G207 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1316 | 29% helix, 22% strand | P0A8V4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1336 | 35% helix, 17% strand | A0A4S1NBU2 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 61% helix, 0% strand | P0A802 |
| R | RNA (20-mer) | rna | 10 | — | — |
| P | DNA (64-mer) | dna | 55 | — | — |
| Q | DNA (64-mer) | dna | 48 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, J, R
- ZN · Zinc ion · metal · 2 copies · chains J
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 | 850 | 0.83 | 0.85 | 75 | empty |
| 2 | 777 | 0.83 | 0.86 | 90 | empty |
| 3 | 887 | 0.82 | 0.84 | 78 | empty |
| 4 | 920 | 0.78 | 0.81 | 95 | empty |
| 5 | 586 | 0.78 | 0.84 | 50 | empty |
Interfaces
19 interfaces between chains.
- I–J · 8275 Ų buried · 93 hydrogen bonds · protein-protein
- G–H · 2122 Ų buried · 11 hydrogen bonds · protein-protein
- P–Q · 2052 Ų buried · 168 hydrogen bonds · nucleic-nucleic
- G–I · 1824 Ų buried · 22 hydrogen bonds · protein-protein
- A–I · 1523 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6X4Y · Mfd-bound E.coli RNA polymerase elongation complex - IV state · the same entry in another collection · chain Q against Q, TM-score 1.00
- P0A802 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A802) · a predicted model of the same protein · chain K against A, TM-score 0.95
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 A0A024L3Y3
- Every structure of UniProt A0A073G207
- Every structure of UniProt P0A8V4
- Every structure of UniProt A0A4S1NBU2
- Every structure of UniProt P0A802
- Elsewhere: RCSB PDB 6X4Y · PDBe 6X4Y · UniProt A0A024L3Y3 · UniProt A0A073G207 · UniProt P0A8V4 · UniProt A0A4S1NBU2 · UniProt P0A802
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