Research workbench
Crystal structure of thermus thermophilus card in complex with the thermus aquaticus RNA polymerase BETA1 domain
Analyse Crystal structure of thermus thermophilus card in complex with the thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XAX
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit beta domain 1; Card
- EC
- 2.7.7.6
- UniProt
- Q9KWU7, Q5SLX5
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit beta domain 1 (EC 2.7.7.6) | protein | 184 | 35% helix, 23% strand | Q9KWU7 |
| B | Card | protein | 158 | 48% helix, 21% strand | Q5SLX5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.63 | 0.83 | 44 | EDO |
| 2 | 127 | 0.43 | 0.76 | 18 | empty |
| 3 | 53 | 0.33 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 662 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4XAX · Crystal structure of Thermus thermophilus CarD in complex with the Thermus aquaticus RNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KWU7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q9KWU7) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9KWU7
- Every structure of UniProt Q5SLX5
- Elsewhere: RCSB PDB 4XAX · PDBe 4XAX · UniProt Q9KWU7 · UniProt Q5SLX5
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