MolNFT v1 · #69004 · protein + DNA
Closed binary complex of an RB69 GP43 fingers domain mutant complexed with an acyclic gmp terminated primer template pair.
3KD1 · DNA (5'- D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*…: “Closed binary complex of an RB69 GP43 fingers domain mutant complexed with an acyclic gmp terminated primer…”. X-ray diffraction, 2 ligands (4DG, MG), 10 pockets (best…
- 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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