Research workbench
Post-catalytic nicked complex of DNA polymerase lambda with bound mismatched dsb substrate
Analyse Post-catalytic nicked complex of DNA polymerase lambda with bound mismatched… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M0C
- Type
- protein + DNA
- Length
- 354 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*AP*G)-3'); DNA (5'-D(*TP*AP*CP*TP*G)-3')…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- PPV, MG, NA, CL, SO4
- Pockets
- 4 · best druggability 0.68
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 | 332 | 51% helix, 12% strand | Q9UGP5 |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*G)-3') | dna | 6 | — | — |
| U | DNA (5'-D(*TP*AP*CP*TP*G)-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 | — | — |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains A, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P, D
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.68 | 0.82 | 35 | CL |
| 2 | 969 | 0.68 | 0.74 | 58 | MG, PPV |
| 3 | 118 | 0.65 | 0.88 | 30 | empty |
| 4 | 122 | 0.48 | 0.80 | 23 | empty |
Interfaces
8 interfaces between chains.
- A–P · 549 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–T · 467 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 384 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–U · 382 Ų buried · 6 hydrogen bonds · protein-nucleic
- U–P · 245 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
- 7M0C · Post-catalytic nicked complex of DNA Polymerase Lambda with bound mismatched 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 7M0C · PDBe 7M0C · UniProt Q9UGP5
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