MolNFT v1 · #78871 · protein + DNA
Crystal structure of the K131A mutant of lambda exonuclease in complex with a 5'-phosphorylated 14-MER/12-mer duplex and magnesium
3SM4: “Crystal structure of the K131A mutant of lambda exonuclease in complex with a 5'-phosphorylated 14-MER/12-mer…”. X-ray diffraction, 3 ligands (MG, PO4, CL), 12 pockets (best druggability 0.83). MolNFT v1 #78871 on GenesisL1: 3D…
- PDB
- 3SM4
- Type
- protein + DNA
- Length
- 708 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease; 5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'…
- EC
- 3.1.11.3
- UniProt
- P03697
- Ligands
- MG, PO4, CL
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exonuclease (EC 3.1.11.3) | protein | 225 | 51% helix, 14% strand | P03697 |
| B | Exonuclease (EC 3.1.11.3) | protein | 228 | 49% helix, 14% strand | P03697 |
| C | Exonuclease (EC 3.1.11.3) | protein | 229 | 50% helix, 14% strand | P03697 |
| D | 5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3' | dna | 12 | — | — |
| E | 5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3' | dna | 14 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, E
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.83 | 0.84 | 79 | empty |
| 2 | 777 | 0.77 | 0.81 | 78 | PO4, CL |
| 3 | 610 | 0.75 | 0.82 | 60 | PO4 |
| 4 | 421 | 0.67 | 0.80 | 38 | empty |
| 5 | 126 | 0.53 | 0.82 | 23 | MG |
Interfaces
10 interfaces between chains.
- B–E · 763 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 678 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 636 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 549 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Compared structures
- 3SM4 · Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
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 P03697
- Elsewhere: RCSB PDB 3SM4 · PDBe 3SM4 · UniProt P03697
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