Research workbench
E. COLI (lacz) beta-galactosidase (N460S) in complex with galactotetrazole
Analyse E. COLI (lacz) beta-galactosidase (N460S) in complex with galactotetrazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VD7
- 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
- P00722
- Ligands
- GTZ, NA, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1011 | 13% helix, 41% strand | P00722 |
Ligands and binding sites
- GTZ · (5R, 6S, 7S, 8S)-5-hydroxymethyl-6,7,8-trihydroxy-tetrazolo[1,5-a]piperidine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 29 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 | 1051 | 0.82 | 0.84 | 93 | empty |
| 2 | 1042 | 0.82 | 0.83 | 112 | empty |
| 3 | 678 | 0.79 | 0.84 | 102 | DMS |
| 4 | 530 | 0.78 | 0.85 | 90 | DMS |
| 5 | 453 | 0.73 | 0.83 | 42 | DMS |
Interfaces
6 interfaces between chains.
- A–D · 2370 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2366 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2109 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2094 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 116 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3VD7 · E. coli (lacZ) beta-galactosidase (N460S) in complex with galactotetrazole · the same entry in another collection · chain D against D, TM-score 1.00
- P00722 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00722) · a predicted model of the same protein · chain D 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 P00722
- Elsewhere: RCSB PDB 3VD7 · PDBe 3VD7 · UniProt P00722
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