MolNFT v1 · #78860 · protein + DNA
Crystal structure of lambda exonuclease in complex with a 12 bp symmetric DNA duplex
3SLP: “Crystal structure of lambda exonuclease in complex with a 12 bp symmetric DNA duplex”. X-ray diffraction, 3 ligands (CA, PO4, CL), 12 pockets (best druggability 0.81). MolNFT v1 #78860 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3SLP
- Type
- protein + DNA
- Length
- 702 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease; 5'-D(*GP*CP*GP*AP*CP*TP*AP*GP*TP*CP*GP*C)-3'
- EC
- 3.1.11.3
- UniProt
- P03697
- Ligands
- CA, PO4, CL
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Exonuclease (EC 3.1.11.3) | protein | 226 | 52% helix, 14% strand | P03697 |
| D, E | 5'-D(*GP*CP*GP*AP*CP*TP*AP*GP*TP*CP*GP*C)-3' | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains B, E, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.81 | 0.87 | 67 | CA, PO4 |
| 2 | 919 | 0.76 | 0.79 | 89 | CA, PO4 |
| 3 | 254 | 0.71 | 0.86 | 33 | CA, PO4 |
| 4 | 75 | 0.51 | 0.85 | 18 | empty |
| 5 | 60 | 0.50 | 0.86 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–B · 616 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 613 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 609 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 542 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- B–E · 362 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3SLP · Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex · 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 3SLP · PDBe 3SLP · UniProt P03697
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