MolNFT v1 · #66863 · protein
E. COLI (lacz) beta-galactosidase (M542A) in complex with iptg
3I3D: “E. COLI (lacz) beta-galactosidase (M542A) in complex with iptg”. X-ray diffraction, 3 ligands (IPT, NA, MG), 20 pockets (best druggability 0.82). MolNFT v1 #66863 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3I3D
- Type
- protein
- Length
- 4,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- B8LFD6
- Ligands
- IPT, NA, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1011 | 14% helix, 41% strand | B8LFD6 |
Ligands and binding sites
- IPT · 1-methylethyl 1-thio-beta-D-galactopyranoside · ligand · 6 copies · chains A, B, C, D
- NA · Sodium ion · metal · 17 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 13 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 149 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.82 | 0.83 | 110 | empty |
| 2 | 1008 | 0.82 | 0.83 | 108 | empty |
| 3 | 1137 | 0.76 | 0.78 | 103 | DMS |
| 4 | 1114 | 0.76 | 0.78 | 99 | DMS |
| 5 | 1119 | 0.76 | 0.78 | 110 | DMS |
Interfaces
6 interfaces between chains.
- B–C · 2294 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2174 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2027 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2018 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 148 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3I3D · E. COLI (lacZ) BETA-GALACTOSIDASE (M542A) IN COMPLEX WITH IPTG · 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 B8LFD6
- Elsewhere: RCSB PDB 3I3D · PDBe 3I3D · UniProt B8LFD6
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