Research workbench
E. COLI (lacz) beta-galactosidase (E416V)
Analyse E. COLI (lacz) beta-galactosidase (E416V) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IAQ
- 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
- 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 | B8LFD6 |
Ligands and binding sites
- NA · Sodium ion · metal · 14 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 13 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 91 copies · chains A, D, B, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
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 | 1114 | 0.82 | 0.83 | 123 | empty |
| 2 | 1055 | 0.82 | 0.83 | 124 | empty |
| 3 | 1081 | 0.76 | 0.78 | 99 | DMS |
| 4 | 1160 | 0.76 | 0.78 | 111 | DMS |
| 5 | 409 | 0.72 | 0.83 | 44 | DMS |
Interfaces
6 interfaces between chains.
- A–D · 2445 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2413 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2139 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2104 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 133 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3IAQ · E. coli (lacz) beta-galactosidase (E416V) · 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 3IAQ · PDBe 3IAQ · UniProt B8LFD6
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