Research workbench
DNA polymerase lambda, TTPAS:AT MN2+ product state ternary complex, 60 min
Analyse DNA polymerase lambda, TTPAS:AT MN2+ product state ternary complex, 60 min in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M4L
- Type
- protein + DNA
- Length
- 341 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- YQS, PPV, MN, NA
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 320 | 50% helix, 15% strand | Q9UGP5 |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*CP*AP*GP*TP*AP*CP*(YQS))-3') | dna | 6 | — | — |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- YQS · [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, T, P
- PPV · Pyrophosphate · ligand · chains A, P
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.67 | 0.75 | 57 | YQS, MN, PPV |
| 2 | 170 | 0.56 | 0.81 | 26 | empty |
| 3 | 262 | 0.49 | 0.74 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–T · 837 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 380 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–P · 369 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 283 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- T–D · 190 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7M4L · DNA Polymerase Lambda, TTPaS:At Mn2+ Product State Ternary Complex, 60 min · 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 7M4L · PDBe 7M4L · UniProt Q9UGP5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.