Research workbench
Closed binary complex of an RB69 GP43 fingers domain mutant complexed with an acyclic gmp terminated primer template pair.
Analyse Closed binary complex of an RB69 GP43 fingers domain mutant complexed with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KD1
- Type
- protein + DNA
- Length
- 936 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- 4DG, MG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'- D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
| P | DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))- 3') | dna | 13 | — | — |
| E | DNA polymerase (EC 2.7.7.7) | protein | 905 | 44% helix, 19% strand | Q38087 |
Ligands and binding sites
- 4DG · 2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) methoxy]ethyl dihydrogen phosphate · ligand · chains T, P, E
- MG · Magnesium ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.84 | 0.92 | 36 | empty |
| 2 | 708 | 0.78 | 0.82 | 73 | 4DG |
| 3 | 838 | 0.78 | 0.81 | 69 | MG |
| 4 | 368 | 0.63 | 0.78 | 43 | empty |
| 5 | 311 | 0.60 | 0.78 | 37 | empty |
Interfaces
3 interfaces between chains.
- T–E · 1359 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–E · 676 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 601 Ų buried · 57 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3KD1 · Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP… · the same entry in another collection · chain T against T, 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 Q38087
- Elsewhere: RCSB PDB 3KD1 · PDBe 3KD1 · UniProt Q38087
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