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Crystal structure of T.AQUATICUS transcription initiation complex containing upstream fork (-11 base-paired) 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
- 4XLQ
- Type
- protein + DNA
- Length
- 6,976 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 0.87
Structure
x-ray diffraction · 9 distinct chains · 35% helix, 18% 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 | 21% helix, 28% strand | Q9KWU8 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1112 | 25% helix, 20% strand | Q9KWU7 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1490 | 35% helix, 19% strand | Q9KWU6 |
| E, K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 93 | 42% helix, 9% strand | Q9EVV4 |
| F, L | RNA polymerase sigma factor siga | protein | 345 | 61% helix, 1% strand | Q9EZJ8 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1367 | 38% helix, 18% strand | Q9KWU6 |
| O, R | DNA (30-mer) | dna | 30 | — | — |
| P | DNA (26-mer) | dna | 25 | — | — |
| S | DNA (26-mer) | dna | 26 | — | — |
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 | 1064 | 0.87 | 0.88 | 107 | empty |
| 2 | 632 | 0.85 | 0.90 | 72 | empty |
| 3 | 1035 | 0.84 | 0.85 | 122 | empty |
| 4 | 262 | 0.82 | 0.93 | 31 | empty |
| 5 | 882 | 0.82 | 0.84 | 92 | empty |
Interfaces
35 interfaces between chains.
- I–J · 8879 Ų buried · 128 hydrogen bonds · protein-protein
- C–D · 8840 Ų buried · 134 hydrogen bonds · protein-protein
- J–L · 4109 Ų buried · 49 hydrogen bonds · protein-protein
- D–F · 4081 Ų buried · 52 hydrogen bonds · protein-protein
- I–L · 2578 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4XLQ · 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 4XLQ · PDBe 4XLQ · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4 · UniProt Q9EZJ8
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