MolNFT v1 · #27739 · protein + DNA
Crystal structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddttp
1XSN · 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3': “Crystal structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddttp”. X-ray diffraction, 3 ligands (D3T, NA, MG), 4 pockets (best druggability 0.70). MolNFT…
- PDB
- 1XSN
- Type
- protein + DNA
- Length
- 345 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'; 5'-D(*CP*AP*GP*TP*AP*(2DT))-3'…
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- D3T, NA, MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3' | dna | 11 | — | — |
| P | 5'-D(*CP*AP*GP*TP*AP*(2DT))-3' | dna | 6 | — | — |
| D | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
| A | DNA polymerase lambda (EC 2.7.7.7) | protein | 324 | 45% helix, 15% strand | Q9UGP5 |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains T, P, A
- NA · Sodium ion · metal · 2 copies · chains P, A, T
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains T, D, P, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.70 | 0.75 | 59 | EDO, MG, D3T |
| 2 | 92 | 0.53 | 0.84 | 30 | empty |
| 3 | 312 | 0.52 | 0.74 | 30 | empty |
| 4 | 130 | 0.51 | 0.81 | 22 | EDO |
Interfaces
5 interfaces between chains.
- T–A · 936 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–A · 387 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–A · 373 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–P · 285 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- T–D · 190 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1XSN · Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap… · the same entry in another collection · chain T against T, 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 1XSN · PDBe 1XSN · UniProt Q9UGP5
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