Research workbench
Transcription antitermination factor Q21 in complex with Q21-binding- element DNA
Analyse Transcription antitermination factor Q21 in complex with Q21-binding- element… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P1A
- Type
- protein + DNA
- Length
- 534 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Q protein; DNA (5'- D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)…
- UniProt
- Q9XJQ6
- Ligands
- CL
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Q protein | protein | 152 | 67% helix, 4% strand | Q9XJQ6 |
| B | Q protein | protein | 147 | 66% helix, 3% strand | Q9XJQ6 |
| C | Q protein | protein | 151 | 66% helix, 4% strand | Q9XJQ6 |
| D, F | DNA (5'- D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)- 3') | dna | 21 | — | — |
| E, G | DNA (5'- D(*CP*TP*TP*GP*CP*TP*CP*AP*TP*TP*TP*GP*CP*TP*CP*AP*AP*TP*GP*AP*G)- 3') | dna | 21 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.64 | 0.75 | 57 | CL |
| 2 | 445 | 0.61 | 0.76 | 53 | EDO |
| 3 | 118 | 0.43 | 0.77 | 28 | empty |
| 4 | 148 | 0.41 | 0.74 | 24 | empty |
| 5 | 129 | 0.38 | 0.74 | 16 | empty |
Interfaces
12 interfaces between chains.
- F–G · 930 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- D–E · 927 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–C · 501 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 488 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 480 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6P1A · Transcription antitermination factor Q21 in complex with Q21-binding-element DNA · the same entry in another collection · chain A against A, 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 Q9XJQ6
- Elsewhere: RCSB PDB 6P1A · PDBe 6P1A · UniProt Q9XJQ6
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