MolNFT v1 · #137227 · protein + DNA + RNA
Structure of mycobacterium smegmatis transcription initiation complex with a full transcription bubble
5VI5 · DNA (49-mer): “Structure of mycobacterium smegmatis transcription initiation complex with a full transcription bubble”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #137227 on GenesisL1: 3D…
- PDB
- 5VI5
- Type
- protein + DNA + RNA
- Length
- 3,377 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (49-mer); DNA (44-mer); RNA (5'-R(*UP*CP*GP*A)-3'); DNA-directed RNA polymerase…
- EC
- 2.7.7.6
- UniProt
- A0QSL8, P60281, A0QS66, A0QWT1, A0QW02, A0QZ11
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 10 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | DNA (49-mer) | dna | 49 | — | — |
| P | DNA (44-mer) | dna | 44 | — | — |
| Q | RNA (5'-R(*UP*CP*GP*A)-3') | rna | 4 | — | — |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 19% helix, 37% strand | A0QSL8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 22% helix, 38% strand | A0QSL8 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1113 | 25% helix, 24% strand | P60281 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1238 | 45% helix, 13% strand | A0QS66 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 43% helix, 5% strand | A0QWT1 |
| F | RNA polymerase sigma factor siga | protein | 314 | 71% helix, 2% strand | A0QW02 |
| J | RNA polymerase-binding protein rbpa | protein | 86 | 33% helix, 26% strand | A0QZ11 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D
- SO4 · Sulfate ion · ion · 6 copies · chains C, D, F
- EDO · 1,2-ethanediol · additive · 2 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 | 762 | 0.81 | 0.84 | 90 | empty |
| 2 | 679 | 0.81 | 0.86 | 54 | empty |
| 3 | 462 | 0.80 | 0.88 | 52 | empty |
| 4 | 708 | 0.80 | 0.85 | 67 | empty |
| 5 | 864 | 0.79 | 0.82 | 94 | SO4 |
Interfaces
24 interfaces between chains.
- C–D · 7996 Ų buried · 98 hydrogen bonds · protein-protein
- D–F · 2652 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2151 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 2030 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 1909 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5VI5 · Structure of Mycobacterium smegmatis transcription initiation complex with a full… · the same entry in another collection · chain J against J, 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 0.98
- A0QS66 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (A0QS66) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 5VI5 · PDBe 5VI5 · UniProt A0QSL8 · UniProt P60281 · UniProt A0QS66 · UniProt A0QWT1 · UniProt A0QW02 · UniProt A0QZ11
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