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Crystal structure of T.AQUATICUS transcription initiation complex containing upstream fork promoter
Analyse Crystal structure of T.AQUATICUS transcription initiation complex containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XLP
- Type
- protein + DNA
- Length
- 6,975 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
- UniProt
- Q9KWU8, Q9KWU7, Q9KWU6, Q9EVV4, Q9EZJ8
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 19% helix, 35% strand | Q9KWU8 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1112 | 27% helix, 24% strand | Q9KWU7 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1490 | 36% helix, 22% strand | Q9KWU6 |
| E, K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 93 | 51% helix, 10% strand | Q9EVV4 |
| F, L | RNA polymerase sigma factor siga | protein | 345 | 69% helix, 1% strand | Q9EZJ8 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1367 | 39% helix, 19% strand | Q9KWU6 |
| O, R | DNA (30-mer) | dna | 30 | — | — |
| P, S | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
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 | 956 | 0.86 | 0.88 | 95 | empty |
| 2 | 1008 | 0.86 | 0.87 | 100 | empty |
| 3 | 928 | 0.83 | 0.84 | 94 | empty |
| 4 | 860 | 0.82 | 0.85 | 102 | empty |
| 5 | 289 | 0.78 | 0.89 | 41 | empty |
Interfaces
33 interfaces between chains.
- C–D · 8844 Ų buried · 112 hydrogen bonds · protein-protein
- I–J · 8830 Ų buried · 112 hydrogen bonds · protein-protein
- J–L · 4107 Ų buried · 48 hydrogen bonds · protein-protein
- D–F · 4052 Ų buried · 48 hydrogen bonds · protein-protein
- I–L · 2377 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4XLP · Crystal structure of T.aquaticus transcription initiation complex containing upstream… · the same entry in another collection · chain S against S, 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 Q9KWU8
- Every structure of UniProt Q9KWU7
- Every structure of UniProt Q9KWU6
- Every structure of UniProt Q9EVV4
- Every structure of UniProt Q9EZJ8
- Elsewhere: RCSB PDB 4XLP · PDBe 4XLP · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4 · UniProt Q9EZJ8
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