Research workbench
Crystal structure of a restriction enzyme pabi in complex with DNA
Analyse Crystal structure of a restriction enzyme pabi in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WAZ
- Type
- protein + DNA
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; DNA (5'-D(*GP*CP*AP*TP*AP*GP*CP*TP*GP*TP*(ORP)…
- UniProt
- Q9V2B6
- Ligands
- ORP, ADE
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 216 | 25% helix, 35% strand | Q9V2B6 |
| B | Putative uncharacterized protein | protein | 217 | 29% helix, 36% strand | Q9V2B6 |
| C, D | DNA (5'-D(*GP*CP*AP*TP*AP*GP*CP*TP*GP*TP*(ORP) P*CP*AP*GP*CP*TP*AP*TP*GP*C)-3') | dna | 19 | — | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · 2 copies · chains B, C, A, D
- ADE · Adenine · ligand · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.78 | 0.88 | 41 | empty |
| 2 | 81 | 0.71 | 0.95 | 23 | empty |
| 3 | 70 | 0.70 | 0.95 | 18 | empty |
| 4 | 106 | 0.44 | 0.78 | 20 | ORP, ADE |
| 5 | 115 | 0.44 | 0.78 | 20 | ORP, ADE |
Interfaces
6 interfaces between chains.
- A–B · 2183 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 740 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- A–D · 706 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 693 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–D · 416 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3WAZ · Crystal structure of a restriction enzyme PabI in complex with 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 Q9V2B6
- Elsewhere: RCSB PDB 3WAZ · PDBe 3WAZ · UniProt Q9V2B6
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