MolNFT v1 · #109181 · protein + DNA
Crystal structure of lambda exonuclease in complex with DNA and CA2+
4WUZ: “Crystal structure of lambda exonuclease in complex with DNA and CA2+”. X-ray diffraction, 2 ligands (CA, PO4), 12 pockets (best druggability 0.82). MolNFT v1 #109181 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WUZ
- Type
- protein + DNA
- Length
- 703 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease; DNA (5'-D(*TP*T*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'); DNA…
- EC
- 3.1.11.3
- UniProt
- P03697
- Ligands
- CA, PO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exonuclease (EC 3.1.11.3) | protein | 226 | 50% helix, 14% strand | P03697 |
| C | Exonuclease (EC 3.1.11.3) | protein | 225 | 50% helix, 14% strand | P03697 |
| D | DNA (5'-D(*TP*T*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3') | dna | 12 | — | — |
| E | DNA (5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3') | dna | 14 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, E, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.82 | 0.89 | 48 | empty |
| 2 | 758 | 0.78 | 0.82 | 77 | CA, PO4 |
| 3 | 223 | 0.71 | 0.87 | 33 | PO4, CA |
| 4 | 165 | 0.65 | 0.86 | 26 | empty |
| 5 | 115 | 0.63 | 0.88 | 23 | empty |
Interfaces
10 interfaces between chains.
- B–E · 734 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 630 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 624 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 538 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Compared structures
- 4WUZ · Crystal structure of lambda exonuclease in complex with DNA and Ca2+ · 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 4WUZ · PDBe 4WUZ · UniProt P03697
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