Research workbench
Crystal structure of the R.PABI(Y68F-K154A)-DSDNA(GTAC-5BP-gtac) complex
Analyse Crystal structure of the R.PABI(Y68F-K154A)-DSDNA(GTAC-5BP-gtac) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L2O
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RE_R_PAB1 domain-containing protein; DNA (5'- D(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*…
- UniProt
- Q9V2B6
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RE_R_PAB1 domain-containing protein | protein | 217 | 29% helix, 37% strand | Q9V2B6 |
| B | RE_R_PAB1 domain-containing protein | protein | 212 | 30% helix, 34% strand | Q9V2B6 |
| C | DNA (5'- D(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*G )-3') | dna | 20 | — | — |
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 | 1092 | 0.76 | 0.78 | 93 | empty |
| 2 | 69 | 0.35 | 0.77 | 15 | empty |
| 3 | 58 | 0.27 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1884 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 349 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 340 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6L2O · Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-5bp-GTAC) complex · 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 Q9V2B6
- Elsewhere: RCSB PDB 6L2O · PDBe 6L2O · UniProt Q9V2B6
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