MolNFT v1 · #116439 · protein + DNA
Human DNA polymerase lambda- apoenzyme and complex with 6 paired DNA
5DDM: “Human DNA polymerase lambda- apoenzyme and complex with 6 paired DNA”. X-ray diffraction, 2 ligands (NA, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #116439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DDM
- 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
- NA, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase lambda (EC 2.7.7.7) | protein | 247 | 43% helix, 22% strand | Q9UGP5 |
| A | DNA polymerase lambda (EC 2.7.7.7) | protein | 242 | 38% helix, 21% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.69 | 0.90 | 25 | empty |
| 2 | 708 | 0.68 | 0.76 | 58 | NA |
| 3 | 104 | 0.33 | 0.73 | 26 | SO4 |
Interfaces
4 interfaces between chains.
- B–T · 596 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–A · 563 Ų buried · 8 hydrogen bonds · protein-protein
- B–P · 530 Ų buried · 18 hydrogen bonds · protein-nucleic
- P–T · 289 Ų buried · 20 hydrogen bonds · nucleic-nucleic
Compared structures
- 5DDM · Human DNA polymerase lambda- Apoenzyme and complex with 6 paired DNA · the same entry in another collection · chain B against B, 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 5DDM · PDBe 5DDM · UniProt Q9UGP5
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