MolNFT v1 · #110077 · protein + DNA + RNA
Crystal structure of T.AQUATICUS transcription initiation complex with card containing bubble promoter and RNA
4XLR · DNA-directed RNA polymerase subunit alpha: “Crystal structure of T.AQUATICUS transcription initiation complex with card containing bubble promoter and RNA”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88).…
- 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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