Research workbench
RB69 DNA polymerase triple MUTANT(L561A/S565G/Y567A) ternary complex with dupnpp and a dideoxy-terminated primer in the presence of CA2+
Analyse RB69 DNA polymerase triple MUTANT(L561A/S565G/Y567A) ternary complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S9H
- Type
- protein + DNA
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G) -3'…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DUP, CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G) -3' | dna | 18 | — | — |
| P | 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3' | dna | 13 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 44% helix, 19% strand | Q38087 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains T, P, A
- CA · Calcium ion · metal · 7 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.81 | 0.92 | 35 | empty |
| 2 | 797 | 0.80 | 0.83 | 82 | CA |
| 3 | 615 | 0.75 | 0.82 | 52 | DUP, CA |
| 4 | 406 | 0.64 | 0.78 | 47 | empty |
| 5 | 127 | 0.59 | 0.85 | 17 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1317 Ų buried · 26 hydrogen bonds · protein-nucleic
- P–A · 646 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 612 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3S9H · RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary complex with dUpNpp and a… · 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 3S9H · PDBe 3S9H · UniProt Q38087
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