MolNFT v1 · #115881 · protein + DNA
Crystal structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dctp
5CWR: “Crystal structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and…”. X-ray diffraction, 2 ligands (DCP, CA), 8 pockets (best druggability 0.80). MolNFT v1 #115881 on GenesisL1: 3D structure…
- PDB
- 5CWR
- Type
- protein + DNA
- Length
- 690 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- DCP, CA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7) | protein | 325 | 48% helix, 14% strand | Q9UGP5 |
| T, F | DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
| P, E | DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') | dna | 6 | — | — |
| B | DNA polymerase lambda (EC 2.7.7.7) | protein | 323 | 50% helix, 15% strand | Q9UGP5 |
| D, C | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, T, P, B, F, E
- CA · Calcium ion · metal · 4 copies · chains A, P, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.80 | 0.87 | 74 | empty |
| 2 | 574 | 0.70 | 0.79 | 48 | DCP, CA |
| 3 | 386 | 0.69 | 0.82 | 49 | DCP |
| 4 | 344 | 0.69 | 0.83 | 47 | empty |
| 5 | 270 | 0.57 | 0.78 | 31 | empty |
Interfaces
15 interfaces between chains.
- A–T · 757 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–F · 727 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–D · 392 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 390 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 386 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5CWR · Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one… · the same entry in another collection · chain C against C, 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 0.95
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 5CWR · PDBe 5CWR · UniProt Q9UGP5
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