Research workbench
Bypass of major benzopyrene-dg adduct by Y-family DNA polymerase with unique structural gap
Analyse Bypass of major benzopyrene-dg adduct by Y-family DNA polymerase with unique… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IBK
- Type
- protein + DNA
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*AP*T)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- BAP, POP, CA
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
| D | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*AP*T)-3' | dna | 14 | — | — |
| E | 5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- 3' | dna | 17 | — | — |
Ligands and binding sites
- BAP · 1,2,3-trihydroxy-1,2,3,4-tetrahydrobenzo[a]pyrene · ligand · chains A, E
- POP · Pyrophosphate 2- · ligand · chains A, D
- CA · Calcium ion · metal · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains D, E, A
- GOL · Glycerol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.76 | 0.79 | 72 | BAP, CA, POP |
| 2 | 373 | 0.69 | 0.82 | 39 | EDO |
| 3 | 104 | 0.43 | 0.79 | 19 | EDO |
Interfaces
3 interfaces between chains.
- A–E · 1036 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–D · 671 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–E · 613 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2IBK · Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q97W02
- Elsewhere: RCSB PDB 2IBK · PDBe 2IBK · UniProt Q97W02
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