Research workbench
Incomplete in crystallo incorporation by DNA polymerase lambda bound to blunt-ended dsb substrate and incoming dttp
Analyse Incomplete in crystallo incorporation by DNA polymerase lambda bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M0A
- 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…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- TTP, PPV, NA, MG, CA, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 330 | 51% helix, 12% strand | Q9UGP5 |
| T | DNA (5'-D(*CP*GP*GP*CP*A)-3') | dna | 5 | — | — |
| P | DNA (5'-D(*CP*AP*GP*TP*GP*CP*T)-3') | dna | 7 | — | — |
| 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
- TTP · Thymidine-5'-triphosphate · ligand · chains A, T, P, U
- PPV · Pyrophosphate · ligand · chains A, P
- 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 · 3 copies · chains A
- GOL · Glycerol · additive · chains 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 | 987 | 0.70 | 0.74 | 55 | PPV, NA |
| 2 | 357 | 0.68 | 0.82 | 35 | empty |
| 3 | 122 | 0.63 | 0.87 | 33 | empty |
| 4 | 115 | 0.52 | 0.82 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–P · 548 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–U · 500 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 380 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–T · 361 Ų buried · 5 hydrogen bonds · protein-nucleic
- P–U · 288 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7M0A · Incomplete in crystallo incorporation by DNA Polymerase Lambda bound to blunt-ended DSB… · 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 7M0A · PDBe 7M0A · UniProt Q9UGP5
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