MolNFT v1 · #79419 · protein
E. COLI (lacz) beta-galactosidase (S796D) in complex with iptg
3T2P: “E. COLI (lacz) beta-galactosidase (S796D) in complex with iptg”. X-ray diffraction, 3 ligands (IPT, NA, MG), 20 pockets (best druggability 0.82). MolNFT v1 #79419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3T2P
- Type
- protein
- Length
- 4,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P00722
- Ligands
- IPT, NA, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 1014 | 14% helix, 40% strand | P00722 |
| B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1015 | 14% helix, 41% strand | P00722 |
Ligands and binding sites
- IPT · 1-methylethyl 1-thio-beta-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 10 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 63 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 | 1108 | 0.82 | 0.83 | 127 | empty |
| 2 | 1076 | 0.82 | 0.83 | 104 | empty |
| 3 | 1122 | 0.81 | 0.82 | 146 | DMS |
| 4 | 1083 | 0.76 | 0.78 | 106 | DMS |
| 5 | 1134 | 0.75 | 0.78 | 104 | DMS |
Interfaces
6 interfaces between chains.
- B–C · 2526 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 2466 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2108 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2087 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 132 Ų buried · 4 hydrogen bonds · protein-protein
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 P00722
- Elsewhere: RCSB PDB 3T2P · PDBe 3T2P · UniProt P00722
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