MolNFT v1 · #146874 · protein + DNA
Crystal structure of mycobacterium tuberculosis transcription initiation COMPLEX(ECF selenomethionine-labelled sigma factor L) with 6 nt spacer
6DVE · DNA-directed RNA polymerase subunit alpha: “Crystal structure of mycobacterium tuberculosis transcription initiation COMPLEX(ECF…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #146874 on…
- PDB
- 6DVE
- Type
- protein + DNA
- Length
- 3,139 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 0.83
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 19% helix, 39% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 232 | 19% 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 | 72% helix, 2% strand | P9WGH5 |
| G | DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*T)-3') | dna | 12 | — | — |
| H | DNA (5'- D(P*CP*GP*TP*GP*TP*GP*AP*GP*TP*AP*AP*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 | 646 | 0.83 | 0.87 | 77 | empty |
| 2 | 883 | 0.82 | 0.84 | 77 | empty |
| 3 | 839 | 0.80 | 0.83 | 81 | empty |
| 4 | 353 | 0.74 | 0.86 | 31 | empty |
| 5 | 934 | 0.72 | 0.76 | 80 | empty |
Interfaces
16 interfaces between chains.
- C–D · 8663 Ų buried · 109 hydrogen bonds · protein-protein
- A–B · 2432 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2266 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2120 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 2118 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 6DVE · 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 0.98
- 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 0.94
- 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 6DVE · PDBe 6DVE · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.