MolNFT v1 · #146873 · protein + DNA
Crystal structure of mycobacterium tuberculosis transcription initiation COMPLEX(ECF sigma factor L) with 6 nt spacer and bromine labelled in position "-11
6DVD · DNA-directed RNA polymerase subunit alpha: “Crystal structure of mycobacterium tuberculosis transcription initiation COMPLEX(ECF sigma factor L) with 6…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 6DVD
- Type
- protein + DNA
- Length
- 3,137 residues
- Chains
- 8
- 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
- P9WGZ1, P9WGY9, P9WGY7, P9WGY5, P9WGH5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 17% helix, 39% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 232 | 20% helix, 40% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1126 | 26% helix, 28% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1265 | 45% helix, 14% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 81 | 46% helix, 1% strand | P9WGY5 |
| F | Ecf RNA polymerase sigma factor sigl | protein | 174 | 71% helix, 2% strand | P9WGH5 |
| G | DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*A)-3') | dna | 10 | — | — |
| H | DNA (5'- D(P*CP*GP*TP*GP*TP*CP*AP*GP*TP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP *GP*C)-3') | dna | 24 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D
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 | 851 | 0.84 | 0.87 | 97 | empty |
| 2 | 1127 | 0.82 | 0.83 | 114 | empty |
| 3 | 1099 | 0.80 | 0.82 | 80 | empty |
| 4 | 614 | 0.79 | 0.85 | 70 | empty |
| 5 | 1072 | 0.75 | 0.78 | 99 | empty |
Interfaces
16 interfaces between chains.
- C–D · 8530 Ų buried · 117 hydrogen bonds · protein-protein
- A–B · 2434 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2254 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2139 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 2128 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6DVD · Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF… · the same entry in another collection · chain H against H, TM-score 1.00
- P9WGY9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P9WGY9) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P9WGY5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P9WGY5) · a predicted model of the same protein · chain E against A, TM-score 0.95
- P9WGY7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P9WGY7) · a predicted model of the same protein · chain D against A, TM-score 0.92
- P9WGH5 · AlphaFold monomer V2.0 prediction for ecf RNA polymerase sigma factor sigl (P9WGH5) · a predicted model of the same protein · chain F against A, TM-score 0.45
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 P9WGZ1
- Every structure of UniProt P9WGY9
- Every structure of UniProt P9WGY7
- Every structure of UniProt P9WGY5
- Every structure of UniProt P9WGH5
- Elsewhere: RCSB PDB 6DVD · PDBe 6DVD · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH5
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