MolNFT v1 · #1243 · protein
Toroidal structure of lambda exonuclease determined at 2.4 ångströms
1AVQ: “Toroidal structure of lambda exonuclease determined at 2.4 ångströms”. X-ray diffraction, 1 ligand (PO4), 9 pockets (best druggability 0.75). MolNFT v1 #1243 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1AVQ
- Type
- protein
- Length
- 681 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lambda exonuclease
- EC
- 3.1.11.3
- UniProt
- P03697
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lambda exonuclease (EC 3.1.11.3) | protein | 228 | 49% helix, 14% strand | P03697 |
| C | Lambda exonuclease (EC 3.1.11.3) | protein | 225 | 52% helix, 14% strand | P03697 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.75 | 0.78 | 72 | PO4 |
| 2 | 847 | 0.74 | 0.78 | 72 | PO4 |
| 3 | 832 | 0.72 | 0.77 | 66 | PO4 |
| 4 | 56 | 0.36 | 0.78 | 13 | ACT |
| 5 | 89 | 0.35 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 607 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 594 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1AVQ · Toroidal structure of lambda exonuclease determined at 2.4 ångströms · the same entry in another collection · chain B against B, 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 1AVQ · PDBe 1AVQ · UniProt P03697
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