MolNFT v1 · #136056 · protein + DNA
Crystal structure of mycobacterium tuberculosis transcription initiation complex containing 4NT RNA in complex with rifampin
5UHD · DNA-directed RNA polymerase subunit alpha: “Crystal structure of mycobacterium tuberculosis transcription initiation complex containing 4NT RNA in…”. X-ray diffraction, 3 ligands (RFP, ZN, MG), 20 pockets (best druggability 0.83).…
- PDB
- 5UHD
- Type
- protein + DNA
- Length
- 3,280 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, P9WGI1
- Ligands
- RFP, ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 23% helix, 37% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 20% helix, 38% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1126 | 26% helix, 27% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1265 | 43% helix, 15% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 81 | 52% helix, 4% strand | P9WGY5 |
| F | RNA polymerase sigma factor siga | protein | 320 | 65% helix, 2% strand | P9WGI1 |
| H | DNA (5'- D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP* G)-3') | dna | 23 | — | — |
| G | DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*G)- 3') | dna | 14 | — | — |
Ligands and binding sites
- RFP · Rifampicin · ligand · chains C, G
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · 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 | 1036 | 0.83 | 0.84 | 91 | empty |
| 2 | 705 | 0.81 | 0.85 | 80 | empty |
| 3 | 433 | 0.80 | 0.89 | 43 | empty |
| 4 | 847 | 0.80 | 0.83 | 84 | empty |
| 5 | 368 | 0.76 | 0.86 | 36 | empty |
Interfaces
17 interfaces between chains.
- C–D · 8549 Ų buried · 120 hydrogen bonds · protein-protein
- D–F · 2905 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2514 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 2211 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2134 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5UHD · Crystal structure of Mycobacterium tuberculosis transcription initiation complex… · the same entry in another collection · chain G against G, 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 0.94
- P9WGZ1 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P9WGZ1) · a predicted model of the same protein · chain A 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 0.93
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 P9WGI1
- Elsewhere: RCSB PDB 5UHD · PDBe 5UHD · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGI1
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