MolNFT v1 · #115617 · protein + DNA
Human DNA polymerase lambda L431A mutant- apoenzyme and complex with 6 paired DNA
5CP2: “Human DNA polymerase lambda L431A mutant- apoenzyme and complex with 6 paired DNA”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.66). MolNFT v1 #115617 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5CP2
- Type
- protein + DNA
- Length
- 498 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
- SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7) | protein | 240 | 37% helix, 22% strand | Q9UGP5 |
| B | DNA polymerase lambda (EC 2.7.7.7) | protein | 246 | 43% 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
- SO4 · Sulfate ion · ion · chains A
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 | 642 | 0.66 | 0.76 | 54 | empty |
| 2 | 107 | 0.63 | 0.88 | 22 | empty |
| 3 | 58 | 0.42 | 0.82 | 15 | empty |
| 4 | 75 | 0.30 | 0.73 | 19 | SO4 |
Interfaces
4 interfaces between chains.
- B–T · 568 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–P · 531 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 497 Ų buried · 5 hydrogen bonds · protein-protein
- P–T · 286 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 5CP2 · Human DNA polymerase lambda L431A mutant- Apoenzyme 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 B 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 5CP2 · PDBe 5CP2 · UniProt Q9UGP5
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