Research workbench
Ternary complex of RB69 mutant L415F wit dumpnpp
Analyse Ternary complex of RB69 mutant L415F wit dumpnpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KHQ
- Type
- protein + DNA
- Length
- 931 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'- D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DUP, NA, CA
- 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 |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 899 | 44% helix, 19% strand | Q38087 |
| T | DNA (5'- D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
| P | DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3') | dna | 14 | — | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P
- NA · Sodium ion · metal · 8 copies · chains A, P
- CA · Calcium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.84 | 0.94 | 34 | empty |
| 2 | 947 | 0.77 | 0.80 | 75 | CA, DUP, NA |
| 3 | 1112 | 0.75 | 0.78 | 62 | NA |
| 4 | 416 | 0.59 | 0.75 | 43 | empty |
| 5 | 123 | 0.57 | 0.83 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1115 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–P · 713 Ų buried · 19 hydrogen bonds · protein-nucleic
- T–P · 637 Ų buried · 58 hydrogen bonds · nucleic-nucleic
Compared structures
- 4KHQ · Ternary complex of RB69 mutant L415F wit DUMPNPP · 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 4KHQ · PDBe 4KHQ · UniProt Q38087
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