Research workbench
Product bound structure of exonuclease I at 1.5 ångström resolution
Analyse Product bound structure of exonuclease I at 1.5 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QXF
- Type
- protein
- Length
- 433 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease I
- EC
- 3.1.11.1
- UniProt
- P04995
- Ligands
- TMP, MG, NA
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 433 | 50% helix, 15% strand | P04995 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.60 | 0.77 | 42 | empty |
| 2 | 289 | 0.55 | 0.76 | 36 | MG, NA, TMP |
| 3 | 122 | 0.52 | 0.81 | 20 | empty |
| 4 | 57 | 0.51 | 0.87 | 23 | empty |
| 5 | 144 | 0.42 | 0.75 | 27 | empty |
Compared structures
- 2QXF · Product bound structure of exonuclease I at 1.5 angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P04995 · AlphaFold monomer V2.0 prediction for exodeoxyribonuclease I (P04995) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P04995
- Elsewhere: RCSB PDB 2QXF · PDBe 2QXF · UniProt P04995
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