MolNFT v1 · #79146 · protein + DNA
RB69 DNA polymerase (Y567A) ternary complex with dctp opposite 2AP (gc rich sequence)
3SUP: “RB69 DNA polymerase (Y567A) ternary complex with dctp opposite 2AP (gc rich sequence)”. X-ray diffraction, 2 ligands (DCP, CA), 11 pockets (best druggability 0.82). MolNFT v1 #79146 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3SUP
- Type
- protein + DNA
- Length
- 932 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; 5'-D(P*CP*(2PR)P*TP*CP*GP*CP*CP*GP*CP*CP*GP*CP*GP*CP*GP*G)- 3'…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DCP, CA
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 44% helix, 18% strand | Q38087 |
| T | 5'-D(P*CP*(2PR)P*TP*CP*GP*CP*CP*GP*CP*CP*GP*CP*GP*CP*GP*G)- 3' | dna | 16 | — | — |
| P | 5'-D(*CP*GP*CP*GP*CP*GP*GP*CP*GP*GP*CP*GP*(2DA))-3' | dna | 13 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 5 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 | 346 | 0.82 | 0.92 | 37 | empty |
| 2 | 809 | 0.78 | 0.81 | 61 | CA |
| 3 | 683 | 0.77 | 0.82 | 65 | DCP, CA |
| 4 | 178 | 0.57 | 0.81 | 23 | empty |
| 5 | 114 | 0.54 | 0.83 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1064 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 670 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 594 Ų buried · 61 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3SUP · RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (GC rich sequence) · 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 3SUP · PDBe 3SUP · UniProt Q38087
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