MolNFT v1 · #122219 · protein + DNA
Crystal structure of the DNA polymerase lambda binary complex
5IIO · DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3'): “Crystal structure of the DNA polymerase lambda binary complex”. X-ray diffraction, 1 ligand (NA), 16 pockets (best druggability 0.79). MolNFT v1 #122219 on GenesisL1: 3D…
- PDB
- 5IIO
- Type
- protein + DNA
- Length
- 1,389 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3'); DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- NA
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, F, J, N | DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
| C, G, K, O | DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') | dna | 6 | — | — |
| D, H, L, P | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| A, M | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 327 | 48% helix, 16% strand | Q9UGP5 |
| E | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 325 | 48% helix, 15% strand | Q9UGP5 |
| I | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 48% helix, 15% strand | Q9UGP5 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains C, A, D, G, E, K, I, O, M, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.79 | 0.83 | 82 | empty |
| 2 | 1139 | 0.71 | 0.75 | 56 | empty |
| 3 | 1157 | 0.71 | 0.75 | 60 | empty |
| 4 | 854 | 0.70 | 0.76 | 63 | empty |
| 5 | 715 | 0.69 | 0.77 | 49 | empty |
Interfaces
34 interfaces between chains.
- A–M · 550 Ų buried · 6 hydrogen bonds · protein-protein
- J–I · 526 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–E · 504 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–A · 492 Ų buried · 9 hydrogen bonds · protein-nucleic
- N–M · 484 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified, 1 disulfide (nucleotide modification, disulfide).
Compared structures
- 5IIO · Crystal structure of the DNA polymerase lambda binary complex · the same entry in another collection · chain M against M, TM-score 1.00
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 5IIO · PDBe 5IIO · UniProt Q9UGP5
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