MolNFT v1 · #135333 · protein + DNA
Crystal structure of a mycobacterium smegmatis transcription initiation complex with rbpa
5TW1 · RNA polymerase-binding protein rbpa: “Crystal structure of a mycobacterium smegmatis transcription initiation complex with rbpa”. X-ray diffraction, 3 ligands (ZN, MG, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #135333 on…
- PDB
- 5TW1
- Type
- protein + DNA
- Length
- 3,386 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase-binding protein rbpa; DNA-directed RNA polymerase subunit alpha…
- EC
- 2.7.7.6
- UniProt
- A0QZ11, A0QSL8, P60281, A0QS66, A0QWT1, A0QW02
- Ligands
- ZN, MG, 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 |
|---|---|---|---|---|---|
| J | RNA polymerase-binding protein rbpa | protein | 83 | 27% helix, 23% strand | A0QZ11 |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 19% helix, 38% strand | A0QSL8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 19% helix, 37% strand | A0QSL8 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1099 | 26% helix, 25% strand | P60281 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1248 | 46% helix, 14% 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 | 302 | 72% helix, 2% strand | A0QW02 |
| 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 |
| G | Unknown peptide | protein | 17 | 47% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D
- SO4 · Sulfate ion · ion · 12 copies · chains C, D, F, O
- EDO · 1,2-ethanediol · additive · 6 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 | 813 | 0.81 | 0.83 | 85 | empty |
| 2 | 677 | 0.78 | 0.83 | 82 | empty |
| 3 | 762 | 0.78 | 0.82 | 94 | empty |
| 4 | 674 | 0.78 | 0.83 | 88 | EDO |
| 5 | 393 | 0.74 | 0.85 | 34 | empty |
Interfaces
25 interfaces between chains.
- C–D · 7972 Ų buried · 101 hydrogen bonds · protein-protein
- D–F · 2399 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 2147 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2117 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 2043 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5TW1 · Crystal structure of a Mycobacterium smegmatis transcription initiation complex with RbpA · the same entry in another collection · chain G against G, 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 A0QZ11
- 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
- Elsewhere: RCSB PDB 5TW1 · PDBe 5TW1 · UniProt A0QZ11 · UniProt A0QSL8 · UniProt P60281 · UniProt A0QS66 · UniProt A0QWT1 · UniProt A0QW02
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