MolNFT v1 · #168644 · protein + DNA
E. COLI RNAPS70-sspa-gada DNA complex
6WMU · DNA-directed RNA polymerase subunit alpha: “E. COLI RNAPS70-sspa-gada DNA complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #168644 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WMU
- Type
- protein + DNA
- Length
- 4,207 residues
- Chains
- 12
- 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
- UniProt
- A0A073G207, P0A8V4, P0A8T7, P0A802, Q0P6L9, A0A1X3LEF3
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 12 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 24% helix, 37% strand | A0A073G207 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 38% strand | A0A073G207 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1339 | 29% helix, 23% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1363 | 37% helix, 16% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 87 | 66% helix, 0% strand | P0A802 |
| F | RNA polymerase sigma factor rpod | protein | 471 | 69% helix, 1% strand | Q0P6L9 |
| G | DNA nt-strand | dna | 37 | — | — |
| H | DNA T-strand | dna | 27 | — | — |
| I | DNA nt-strand downstream | dna | 11 | — | — |
| J | DNA T-strand downstream | dna | 11 | — | — |
| K | Stringent starvation protein a | protein | 199 | 58% helix, 6% strand | A0A1X3LEF3 |
| L | Stringent starvation protein a | protein | 204 | 53% helix, 7% strand | A0A1X3LEF3 |
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 | 1113 | 0.84 | 0.85 | 101 | empty |
| 2 | 968 | 0.81 | 0.83 | 111 | empty |
| 3 | 1166 | 0.80 | 0.82 | 85 | empty |
| 4 | 1011 | 0.80 | 0.82 | 109 | empty |
| 5 | 992 | 0.77 | 0.80 | 93 | empty |
Interfaces
25 interfaces between chains.
- C–D · 8138 Ų buried · 100 hydrogen bonds · protein-protein
- D–F · 2650 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2031 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 2018 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1784 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6WMU · E. coli RNAPs70-SspA-gadA DNA complex · the same entry in another collection · chain L against L, 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 A0A073G207
- Every structure of UniProt P0A8V4
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A802
- Every structure of UniProt Q0P6L9
- Every structure of UniProt A0A1X3LEF3
- Elsewhere: RCSB PDB 6WMU · PDBe 6WMU · UniProt A0A073G207 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9 · UniProt A0A1X3LEF3
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