MolNFT v1 · #82133 · protein
E. COLI (lacz) beta-galactosidase (N460S) in complex with iptg
3VD9: “E. COLI (lacz) beta-galactosidase (N460S) in complex with iptg”. X-ray diffraction, 3 ligands (IPT, NA, MG), 20 pockets (best druggability 0.81). MolNFT v1 #82133 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VD9
- Type
- protein
- Length
- 4,061 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 0.81
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1015 | 14% helix, 41% strand | P00722 |
| B | Beta-galactosidase (EC 3.2.1.23) | protein | 1016 | 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 · 16 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 64 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 | 982 | 0.81 | 0.83 | 105 | empty |
| 2 | 716 | 0.81 | 0.85 | 111 | DMS |
| 3 | 694 | 0.81 | 0.85 | 96 | DMS |
| 4 | 926 | 0.81 | 0.83 | 106 | empty |
| 5 | 442 | 0.72 | 0.82 | 43 | DMS |
Interfaces
6 interfaces between chains.
- B–C · 2455 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2377 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2075 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2058 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 155 Ų buried · 5 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 3VD9 · PDBe 3VD9 · UniProt P00722
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