MolNFT v1 · #155291 · protein + DNA
Crystal structure of the R.PABI(Y68F-K154A)-DSDNA(GTAC-3BP-gtac) complex
6L2N · RE_R_PAB1 domain-containing protein: “Crystal structure of the R.PABI(Y68F-K154A)-DSDNA(GTAC-3BP-gtac) complex”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #155291 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6L2N
- Type
- protein + DNA
- Length
- 451 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(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP…
- UniProt
- Q9V2B6
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RE_R_PAB1 domain-containing protein | protein | 217 | 27% helix, 37% strand | Q9V2B6 |
| B | RE_R_PAB1 domain-containing protein | protein | 211 | 29% helix, 35% strand | Q9V2B6 |
| C | DNA (5'- D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP* a)-3') | dna | 23 | — | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.76 | 0.78 | 89 | empty |
| 2 | 80 | 0.36 | 0.76 | 16 | empty |
| 3 | 69 | 0.33 | 0.75 | 13 | empty |
| 4 | 73 | 0.32 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1794 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 360 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6L2N · Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-3bp-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 6L2N · PDBe 6L2N · UniProt Q9V2B6
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