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Structural basis for transcription reactivation by rapa
Analyse Structural basis for transcription reactivation by rapa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S20
- Type
- protein + DNA + RNA
- Length
- 7,689 residues
- Chains
- 16
- 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, 3.6.4.-
- UniProt
- B1X6E7, K0AVA1, K0BCS5, K0BU55, P60240
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 9 distinct chains · 28% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 20% helix, 31% strand | B1X6E7 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1179 | 24% helix, 21% strand | K0AVA1 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1149 | 30% helix, 9% strand | K0BCS5 |
| E, J | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 75 | 31% helix, 0% strand | K0BU55 |
| H | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1173 | 23% helix, 21% strand | K0AVA1 |
| I | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1160 | 31% helix, 9% strand | K0BCS5 |
| K, L | RNA polymerase-associated protein rapa (EC 3.6.4.-) | protein | 961 | 33% helix, 10% strand | P60240 |
| M, O | 5'-D(P*AP*CP*GP*AP*CP*TP*GP*AP*GP*CP*CP*GP*AP*TP*G)-3' | dna | 15 | — | — |
| N, P | 5'-R(P*AP*UP*CP*GP*GP*CP*UP*CP*A)-3' | rna | 9 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains D, L, I, K
- MG · Magnesium ion · metal · 2 copies · chains D, P, I, N
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 | 919 | 0.85 | 0.87 | 114 | empty |
| 2 | 818 | 0.84 | 0.87 | 81 | empty |
| 3 | 1146 | 0.84 | 0.85 | 112 | empty |
| 4 | 1061 | 0.84 | 0.84 | 98 | empty |
| 5 | 859 | 0.83 | 0.86 | 77 | empty |
Interfaces
40 interfaces between chains.
- H–I · 8398 Ų buried · 90 hydrogen bonds · protein-protein
- C–D · 8384 Ų buried · 80 hydrogen bonds · protein-protein
- F–G · 1936 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1923 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1620 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4S20 · Structural basis for transcription reactivation by RapA · the same entry in another collection · chain P against P, TM-score 1.00
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 B1X6E7
- Every structure of UniProt K0AVA1
- Every structure of UniProt K0BCS5
- Every structure of UniProt K0BU55
- Every structure of UniProt P60240
- Elsewhere: RCSB PDB 4S20 · PDBe 4S20 · UniProt B1X6E7 · UniProt K0AVA1 · UniProt K0BCS5 · UniProt K0BU55 · UniProt P60240
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