Research workbench
Crystal structure of T.AQUATICUS transcription initiation complex with card containing bubble promoter and RNA
Analyse Crystal structure of T.AQUATICUS transcription initiation complex with card… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XLR
- Type
- protein + DNA + RNA
- Length
- 7,391 residues
- Chains
- 20
- 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, H9ZP94
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 10 distinct chains · 35% helix, 17% 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, 28% strand | Q9KWU8 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1117 | 24% 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 | 47% helix, 9% strand | Q9EVV4 |
| F, L | RNA polymerase sigma factor siga | protein | 345 | 64% helix, 1% strand | Q9EZJ8 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1367 | 38% helix, 17% strand | Q9KWU6 |
| M, N | Card-like transcriptional regulator | protein | 158 | 43% helix, 12% strand | H9ZP94 |
| O, R | DNA (48-mer) | dna | 48 | — | — |
| P, S | DNA (48-mer) | dna | 48 | — | — |
| Q, T | RNA (5'-R(P*UP*CP*GP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains D, J
- MG · Magnesium ion · metal · 2 copies · chains D, Q, J, T
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 | 1055 | 0.88 | 0.89 | 100 | empty |
| 2 | 1139 | 0.87 | 0.88 | 113 | empty |
| 3 | 1011 | 0.87 | 0.89 | 106 | empty |
| 4 | 1160 | 0.86 | 0.87 | 121 | empty |
| 5 | 324 | 0.86 | 0.95 | 36 | empty |
Interfaces
55 interfaces between chains.
- I–J · 8868 Ų buried · 129 hydrogen bonds · protein-protein
- C–D · 8843 Ų buried · 129 hydrogen bonds · protein-protein
- D–F · 4007 Ų buried · 40 hydrogen bonds · protein-protein
- J–L · 3939 Ų buried · 41 hydrogen bonds · protein-protein
- I–L · 2471 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4XLR · Crystal structure of T.aquaticus transcription initiation complex with CarD containing… · the same entry in another collection · chain R against R, 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
- Every structure of UniProt H9ZP94
- Elsewhere: RCSB PDB 4XLR · PDBe 4XLR · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4 · UniProt Q9EZJ8 · UniProt H9ZP94
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