MolNFT v1 · #71513 · protein + DNA
Binary complex of a DNA polymerase lambda loop mutant
3MGH: “Binary complex of a DNA polymerase lambda loop mutant”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.81). MolNFT v1 #71513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MGH
- Type
- protein + DNA
- Length
- 682 residues
- Chains
- 8
- 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
- NA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 319 | 49% helix, 14% strand | Q9UGP5 |
| T, E | DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
| P, F | DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') | dna | 6 | — | — |
| D, G | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| C | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 321 | 48% helix, 14% strand | Q9UGP5 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, P, C, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.81 | 0.83 | 107 | empty |
| 2 | 1167 | 0.71 | 0.75 | 58 | NA |
| 3 | 175 | 0.67 | 0.87 | 40 | empty |
| 4 | 412 | 0.66 | 0.79 | 44 | empty |
| 5 | 301 | 0.64 | 0.81 | 37 | empty |
Interfaces
15 interfaces between chains.
- C–E · 569 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–T · 566 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–G · 393 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 389 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 388 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 3MGH · PDBe 3MGH · UniProt Q9UGP5
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