Research workbench
DNA polymerase- damaged DNA complex
Analyse DNA polymerase- damaged DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q45
- Type
- protein + DNA
- Length
- 751 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*TP*CP*TP*AP*GP*GP*(RDG)…
- EC
- 2.7.7.7
- UniProt
- Q47155
- Ligands
- 1FZ, MG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 44% helix, 23% strand | Q47155 |
| G, B | DNA (5'-D(*TP*CP*TP*AP*GP*GP*(RDG) P*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 18 | — | — |
| H | DNA (5'- D(*TP*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 14 | — | — |
| C | DNA (5'- D(*TP*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 17 | — | — |
Ligands and binding sites
- 1FZ · 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine · ligand · 2 copies · chains F, G, H, A, B, C
- MG · Magnesium ion · metal · 4 copies · chains F, H, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.82 | 0.84 | 81 | 1FZ, MG |
| 2 | 1012 | 0.80 | 0.82 | 79 | 1FZ, MG |
| 3 | 858 | 0.77 | 0.81 | 61 | empty |
| 4 | 510 | 0.73 | 0.82 | 42 | empty |
| 5 | 56 | 0.34 | 0.77 | 13 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1003 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–G · 950 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 691 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- G–H · 684 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- F–H · 616 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 Q47155
- Elsewhere: RCSB PDB 4Q45 · PDBe 4Q45 · UniProt Q47155
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