Research workbench
Crystal structure of a Y-family DNA polymerase in a ternary complex with DNA substrates and an incoming nucleotide
Analyse Crystal structure of a Y-family DNA polymerase in a ternary 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
- 1JXL
- Type
- protein + DNA
- Length
- 368 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3'; 5'-D(*T*TP*CP*GP*AP*AP*(BRU)P*CP*CP*TP*(BRU)…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DG3, MG, CA
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3' | dna | 12 | — | — |
| T | 5'-D(*T*TP*CP*GP*AP*AP*(BRU)P*CP*CP*TP*(BRU) P*CP*CP*CP*CP*C)-3' | dna | 15 | — | — |
| A | DNA polymerase IV (family Y) (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · chains P, T, A
- MG · Magnesium ion · metal · 3 copies · chains A, P
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains P, T
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 | 1045 | 0.81 | 0.83 | 68 | EDO, CA, MG, DG3 |
| 2 | 606 | 0.73 | 0.80 | 35 | empty |
| 3 | 71 | 0.35 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- T–A · 877 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–T · 526 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- P–A · 489 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1JXL · Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates… · the same entry in another collection · chain P against P, 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 0.97
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 1JXL · PDBe 1JXL · UniProt Q97W02
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