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Ternary crystal structure of a polymerase lambda variant with a gt mispair at the primer terminus and sodium at catalytic metal site
Analyse Ternary crystal structure of a polymerase lambda variant with a gt mispair at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PNC
- Type
- protein + DNA
- Length
- 337 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; 5'-D(*CP*AP*GP*TP*AP*G)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- 1GC, NA, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 316 | 50% helix, 14% strand | Q9UGP5 |
| B | 5'-D(*CP*AP*GP*TP*AP*G)-3' | dna | 6 | — | — |
| C | 5'-D(*CP*GP*GP*CP*CP*TP*TP*AP*CP*TP*G)-3' | dna | 11 | — | — |
| D | 5'-D(*GP*CP*CP*G)-3' | dna | 4 | — | — |
Ligands and binding sites
- 1GC · 2'-deoxy-5'-O-[(R)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]guanosine · ligand · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
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 | 1058 | 0.71 | 0.75 | 57 | 1GC, MG, TRS, NA |
| 2 | 67 | 0.57 | 0.89 | 16 | empty |
| 3 | 280 | 0.52 | 0.75 | 26 | empty |
| 4 | 128 | 0.52 | 0.81 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–C · 750 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 422 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 350 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 292 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- C–D · 191 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Compared structures
- 3PNC · Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer… · 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 0.99
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 3PNC · PDBe 3PNC · UniProt Q9UGP5
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