MolNFT v1 · #71991 · protein
E.COLI (lacz) beta-galactosidase (R599A) in complex with guanidinium
3MV1: “E.COLI (lacz) beta-galactosidase (R599A) in complex with guanidinium”. X-ray diffraction, 3 ligands (GAI, NA, MG), 20 pockets (best druggability 0.81). MolNFT v1 #71991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MV1
- 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
- GAI, NA, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3, 4 | Beta-galactosidase (EC 3.2.1.23) | protein | 1011 | 13% helix, 41% strand | B8LFD6 |
Ligands and binding sites
- GAI · Guanidine · ligand · 4 copies · chains 1, 2, 3, 4
- NA · Sodium ion · metal · 16 copies · chains 1, 2, 3, 4
- MG · Magnesium ion · metal · 12 copies · chains 1, 2, 3, 4
- DMS · Dimethyl sulfoxide · additive · 109 copies · chains 1, 2, 4, 3
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 | 985 | 0.81 | 0.83 | 109 | empty |
| 2 | 1154 | 0.81 | 0.82 | 148 | DMS |
| 3 | 483 | 0.77 | 0.85 | 70 | empty |
| 4 | 1148 | 0.75 | 0.78 | 107 | DMS |
| 5 | 1170 | 0.75 | 0.78 | 105 | DMS |
Interfaces
6 interfaces between chains.
- 2–3 · 2367 Ų buried · 30 hydrogen bonds · protein-protein
- 1–4 · 2339 Ų buried · 32 hydrogen bonds · protein-protein
- 1–2 · 2033 Ų buried · 36 hydrogen bonds · protein-protein
- 3–4 · 2018 Ų buried · 29 hydrogen bonds · protein-protein
- 1–3 · 166 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3MV1 · E.Coli (lacZ) beta-galactosidase (R599A) in complex with Guanidinium · the same entry in another collection · chain 1 against 1, 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 3MV1 · PDBe 3MV1 · UniProt B8LFD6
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