MolNFT v1 · #19109 · protein + DNA
Crystal structure of enterobacteria phage RB69 GP43 DNA polymerase complexed with tetrahydrofuran containing DNA
1Q9X · 5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3': “Crystal structure of enterobacteria phage RB69 GP43 DNA polymerase complexed with tetrahydrofuran containing…”. X-ray diffraction, 3 ligands (DGP, DOC, CA), 20 pockets (best druggability 0.84).…
- PDB
- 1Q9X
- Type
- protein + DNA
- Length
- 3,740 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3'; 5'-AC(TETRAHYDROFURAN)GGTAAGCAGTCCGCGG-3'; DNA…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DGP, DOC, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | 5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3' | dna | 19 | — | — |
| I, J, K, L | 5'-AC(TETRAHYDROFURAN)GGTAAGCAGTCCGCGG-3' | dna | 13 | — | — |
| A, B, C, D | DNA polymerase (EC 2.7.7.7) | protein | 903 | 39% helix, 18% strand | Q38087 |
Ligands and binding sites
- DGP · 2'-deoxyguanosine-5'-monophosphate · ligand · 6 copies · chains F, B, G, C, K, H, D, L, A
- DOC · 2',3'-dideoxycytidine-5'-monophosphate · ligand · 4 copies · chains E, I, A, F, J, B, G, K, C, H, L, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.84 | 0.94 | 31 | empty |
| 2 | 362 | 0.84 | 0.94 | 31 | empty |
| 3 | 335 | 0.84 | 0.94 | 28 | empty |
| 4 | 333 | 0.84 | 0.94 | 35 | empty |
| 5 | 1119 | 0.81 | 0.82 | 88 | empty |
Interfaces
14 interfaces between chains.
- F–B · 1093 Ų buried · 18 hydrogen bonds · protein-nucleic
- G–C · 1083 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–A · 1081 Ų buried · 16 hydrogen bonds · protein-nucleic
- H–D · 1076 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–I · 638 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nucleotide modification).
Compared structures
- 1Q9X · Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with… · the same entry in another collection · chain L against L, 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 1Q9X · PDBe 1Q9X · UniProt Q38087
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