Research workbench
E.COLI rnap-rapa elongation complex
Analyse E.COLI rnap-rapa elongation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M8E
- Type
- protein + DNA + RNA
- Length
- 4,230 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6, 3.6.4.-
- UniProt
- A0A073G207, P0A8V4, D8ED86, P0A802, C3TR27
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 22% helix, 37% strand | A0A073G207 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 19% helix, 33% strand | A0A073G207 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 28% helix, 22% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1337 | 32% helix, 14% strand | D8ED86 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 65% helix, 0% strand | P0A802 |
| F | RNA polymerase-associated protein rapa (EC 3.6.4.-) | protein | 967 | 45% helix, 17% strand | C3TR27 |
| 1 | Nontemplate DNA (39-mer) | dna | 18 | — | — |
| 2 | Template DNA (39-mer) | dna | 22 | — | — |
| 3 | RNA (5'-R(P*AP*UP*CP*GP*GP*CP*UP*CP*A)-3') | rna | 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 | 967 | 0.83 | 0.85 | 101 | empty |
| 2 | 768 | 0.82 | 0.86 | 66 | empty |
| 3 | 837 | 0.80 | 0.83 | 75 | empty |
| 4 | 901 | 0.79 | 0.82 | 96 | empty |
| 5 | 941 | 0.79 | 0.82 | 63 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8253 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 1862 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1700 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1229 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 978 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 A0A073G207
- Every structure of UniProt P0A8V4
- Every structure of UniProt D8ED86
- Every structure of UniProt P0A802
- Every structure of UniProt C3TR27
- Elsewhere: RCSB PDB 7M8E · PDBe 7M8E · UniProt A0A073G207 · UniProt P0A8V4 · UniProt D8ED86 · UniProt P0A802 · UniProt C3TR27
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