Research workbench
Pre-catalytic quaternary complex of DNA polymerase lambda with blunt- ended dsb substrate and incoming dumpnpp
Analyse Pre-catalytic quaternary complex of DNA polymerase lambda with blunt- ended dsb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M09
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(*CP*GP*GP*CP*A)-3'); DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- DUP, NA, MG, CA, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 331 | 51% helix, 13% strand | Q9UGP5 |
| T | DNA (5'-D(*CP*GP*GP*CP*A)-3') | dna | 5 | — | — |
| P | DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') | dna | 6 | — | — |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| U | DNA (5'-D(*GP*CP*AP*CP*TP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P, U
- NA · Sodium ion · metal · 3 copies · chains A, P, D
- MG · Magnesium ion · metal · 2 copies · chains A, P
- CA · Calcium ion · metal · chains A, P
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, P, U
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 | 1112 | 0.70 | 0.75 | 60 | DUP, MG, NA |
| 2 | 382 | 0.69 | 0.82 | 33 | empty |
| 3 | 121 | 0.62 | 0.87 | 33 | empty |
| 4 | 120 | 0.51 | 0.81 | 21 | GOL |
Interfaces
8 interfaces between chains.
- A–U · 494 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–P · 383 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 383 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–T · 357 Ų buried · 5 hydrogen bonds · protein-nucleic
- P–U · 278 Ų buried · 22 hydrogen bonds · nucleic-nucleic
Compared structures
- 7M09 · Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate… · 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 7M09 · PDBe 7M09 · UniProt Q9UGP5
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