MolNFT v1 · #110376 · protein + DNA
Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating a and an incoming dttp
4XUS: “Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating a and an…”. X-ray diffraction, 3 ligands (TTP, DOC, MG), 4 pockets (best druggability 0.70). MolNFT v1 #110376 on GenesisL1: 3D…
- PDB
- 4XUS
- Type
- protein + DNA
- Length
- 343 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(P*GP*CP*CP*G)-3'); DNA (5'-D(*CP*AP*GP*TP*A)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- TTP, DOC, MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 323 | 49% helix, 13% strand | Q9UGP5 |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| P | DNA (5'-D(*CP*AP*GP*TP*A)-3') | dna | 5 | — | — |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains A, T
- DOC · 2',3'-dideoxycytidine-5'-monophosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.70 | 0.75 | 68 | TTP, MG, DOC |
| 2 | 273 | 0.51 | 0.74 | 23 | empty |
| 3 | 71 | 0.37 | 0.79 | 11 | empty |
| 4 | 66 | 0.35 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–T · 938 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 404 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 254 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–T · 248 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- D–T · 195 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4XUS · Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9UGP5
- Elsewhere: RCSB PDB 4XUS · PDBe 4XUS · UniProt Q9UGP5
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