MolNFT v1 · #167801 · protein + DNA
Crystal structure of a mycobacterium smegmatis RNA polymerase transcription initiation complex with antibiotic sorangicin
6VVS · DNA-directed RNA polymerase subunit alpha: “Crystal structure of a mycobacterium smegmatis RNA polymerase transcription initiation complex with…”. X-ray diffraction, 3 ligands (SRN, ZN, SO4), 20 pockets (best druggability 0.81).…
- PDB
- 6VVS
- Type
- protein + DNA
- Length
- 3,387 residues
- Chains
- 11
- Method
- x-ray diffraction
- 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
- A0QSL8, P60281, A0QS66, A0QWT1, A0QW02, A0QZ11
- Ligands
- SRN, ZN, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 11 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 19% helix, 37% strand | A0QSL8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 20% helix, 36% strand | A0QSL8 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1099 | 26% helix, 26% strand | P60281 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1246 | 46% helix, 13% strand | A0QS66 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 47% helix, 5% strand | A0QWT1 |
| F | RNA polymerase sigma factor siga | protein | 305 | 70% helix, 1% strand | A0QW02 |
| G | Unknown | protein | 17 | 41% helix, 0% strand | — |
| J | RNA polymerase-binding protein rbpa | protein | 83 | 27% helix, 23% strand | A0QZ11 |
| O | DNA (31-mer) | dna | 31 | — | — |
| P | DNA (26-mer) | dna | 26 | — | — |
| T | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 53 | 68% helix, 0% strand | A0QSL8 |
Ligands and binding sites
- SRN · Sorangicin A · ligand · chains C, F
- ZN · Zinc ion · metal · 2 copies · chains D
- SO4 · Sulfate ion · ion · 14 copies · chains C, D, E, F
- EDO · 1,2-ethanediol · additive · 7 copies · chains C, D, F
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 | 824 | 0.81 | 0.83 | 96 | empty |
| 2 | 901 | 0.80 | 0.82 | 90 | empty |
| 3 | 109 | 0.77 | 0.97 | 31 | empty |
| 4 | 562 | 0.77 | 0.84 | 77 | SO4 |
| 5 | 449 | 0.75 | 0.84 | 36 | SO4 |
Interfaces
25 interfaces between chains.
- C–D · 7906 Ų buried · 101 hydrogen bonds · protein-protein
- D–F · 2398 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2132 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 2071 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 2021 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6VVS · Crystal structure of a Mycobacterium smegmatis RNA polymerase transcription initiation… · the same entry in another collection · chain T against T, TM-score 1.00
- P60281 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P60281) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 A0QSL8
- Every structure of UniProt P60281
- Every structure of UniProt A0QS66
- Every structure of UniProt A0QWT1
- Every structure of UniProt A0QW02
- Every structure of UniProt A0QZ11
- Elsewhere: RCSB PDB 6VVS · PDBe 6VVS · UniProt A0QSL8 · UniProt P60281 · UniProt A0QS66 · UniProt A0QWT1 · UniProt A0QW02 · UniProt A0QZ11
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.