MolNFT v1 · #181740 · protein + DNA
DNA polymerase lambda, TTP:AT MN2+ product state ternary complex, 60 min
7M4B: “DNA polymerase lambda, TTP:AT MN2+ product state ternary complex, 60 min”. X-ray diffraction, 3 ligands (PPV, MN, NA), 4 pockets (best druggability 0.67). MolNFT v1 #181740 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7M4B
- Type
- protein + DNA
- Length
- 342 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
- PPV, MN, NA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 49% 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 | 49% 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*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
- MN · Manganese (II) ion · metal · 4 copies · chains A, P
- NA · Sodium ion · metal · 3 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
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 | 884 | 0.67 | 0.74 | 56 | MN, PPV, EDO |
| 2 | 169 | 0.54 | 0.80 | 25 | empty |
| 3 | 50 | 0.53 | 0.89 | 15 | empty |
| 4 | 277 | 0.50 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–T · 812 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 539 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 380 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–P · 315 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- T–D · 191 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 7M4B · DNA Polymerase Lambda, TTP: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 7M4B · PDBe 7M4B · UniProt Q9UGP5
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