Research workbench
Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase
Analyse Crystal structure of the ternary complex of the D714A mutant of RB69 DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I9Q
- Type
- protein + DNA
- Length
- 1,780 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'- D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- XG4, CA, NA
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 846 | 42% helix, 20% strand | Q38087 |
| T | DNA (5'- D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
| B | DNA polymerase (EC 2.7.7.7) | protein | 873 | 42% helix, 20% strand | Q38087 |
| P, C | DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3') | dna | 13 | — | — |
| D | DNA (5'- D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 17 | — | — |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · 4 copies · chains A, T, P, B, D, C
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.83 | 0.94 | 33 | empty |
| 2 | 1022 | 0.82 | 0.83 | 101 | XG4, CA |
| 3 | 284 | 0.81 | 0.92 | 36 | empty |
| 4 | 800 | 0.80 | 0.83 | 78 | empty |
| 5 | 321 | 0.72 | 0.85 | 42 | XG4, CA |
Interfaces
7 interfaces between chains.
- B–D · 1381 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–T · 1353 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 654 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 652 Ų buried · 19 hydrogen bonds · protein-nucleic
- T–P · 625 Ų buried · 60 hydrogen bonds · nucleic-nucleic
Compared structures
- 4I9Q · Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase · the same entry in another collection · chain A against A, 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 4I9Q · PDBe 4I9Q · UniProt Q38087
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