Research workbench
Crystal structure of enterobacteria phage RB69 GP43 DNA polymerase complexed with tetrahydrofuran containing DNA
Analyse Crystal structure of enterobacteria phage RB69 GP43 DNA polymerase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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