MolNFT v1 · #122217 · protein + DNA
Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-DG:DA base-pair
5IIM: “Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-DG:DA…”. X-ray diffraction, 2 ligands (DUP, NA), 4 pockets (best druggability 0.65). MolNFT v1 #122217 on GenesisL1: 3D…
- PDB
- 5IIM
- Type
- protein + DNA
- Length
- 347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(P*GP*CP*CP*G)-3'); DNA (5'-D(*CP*AP*GP*TP*AP*A)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- DUP, NA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 49% helix, 14% strand | Q9UGP5 |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| P | DNA (5'-D(*CP*AP*GP*TP*AP*A)-3') | dna | 6 | — | — |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*(8OG)P*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, P, T
- NA · Sodium ion · metal · 2 copies · chains A, P
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 | 556 | 0.65 | 0.77 | 46 | DUP, NA |
| 2 | 238 | 0.54 | 0.77 | 23 | empty |
| 3 | 125 | 0.52 | 0.81 | 24 | empty |
| 4 | 67 | 0.39 | 0.79 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–T · 878 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 394 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 378 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 292 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- D–T · 189 Ų buried · 13 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5IIM · Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda… · 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 5IIM · PDBe 5IIM · UniProt Q9UGP5
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