MolNFT v1 · #115364 · protein + DNA
Human DNA polymerase lambda L431A mutant- mgdgtp binary and complex with 6 paired DNA
5CHG: “Human DNA polymerase lambda L431A mutant- mgdgtp binary and complex with 6 paired DNA”. X-ray diffraction, 3 ligands (DGT, MG, SO4), 4 pockets (best druggability 0.64). MolNFT v1 #115364 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5CHG
- Type
- protein + DNA
- Length
- 501 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'); DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3')
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- DGT, MG, SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7) | protein | 246 | 41% helix, 19% strand | Q9UGP5 |
| B | DNA polymerase lambda (EC 2.7.7.7) | protein | 243 | 38% helix, 22% strand | Q9UGP5 |
| P | DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') | dna | 6 | — | — |
| T | DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, P, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.64 | 0.88 | 25 | empty |
| 2 | 411 | 0.56 | 0.74 | 44 | empty |
| 3 | 177 | 0.53 | 0.79 | 25 | empty |
| 4 | 70 | 0.28 | 0.73 | 15 | MG, DGT |
Interfaces
4 interfaces between chains.
- A–T · 603 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–B · 563 Ų buried · 7 hydrogen bonds · protein-protein
- A–P · 533 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 289 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Compared structures
- 5CHG · Human DNA polymerase lambda L431A mutant- MgdGTP binary and complex with 6 paired DNA · 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 5CHG · PDBe 5CHG · UniProt Q9UGP5
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