MolNFT v1 · #66264 · protein
Crystal structure of exonuclease I in complex with inhibitor bcbp
3HL8 · Exodeoxyribonuclease I: “Crystal structure of exonuclease I in complex with inhibitor bcbp”. X-ray diffraction, 2 ligands (BBP, MG), 6 pockets (best druggability 0.60). MolNFT v1 #66264 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3HL8
- Type
- protein
- Length
- 456 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
- BBP, MG
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 456 | 52% helix, 15% strand | P04995 |
Ligands and binding sites
- BBP · (5R)-3-tert-butyl-1-(6-chloro-1,3-benzothiazol-2-yl)-4,5-dihydro-1H-pyrazol-5-ol · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.60 | 0.77 | 44 | EDO |
| 2 | 87 | 0.54 | 0.85 | 20 | empty |
| 3 | 288 | 0.52 | 0.75 | 36 | MG, EDO |
| 4 | 74 | 0.51 | 0.85 | 26 | empty |
| 5 | 167 | 0.44 | 0.74 | 27 | empty |
Compared structures
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 3HL8 · PDBe 3HL8 · UniProt P04995
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