MolNFT v1 · #145691 · protein

Atomic resolution cryo-EM structure of beta-galactosidase

6CVM: “Atomic resolution cryo-EM structure of beta-galactosidase”. Electron microscopy, 3 ligands (PTQ, MG, NA), 20 pockets (best druggability 0.82). MolNFT v1 #145691 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6CVM
Type: protein
Length: 4,084 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: P00722
Ligands: PTQ, MG, NA
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 14% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-galactosidase (EC 3.2.1.23)	protein	1021	14% helix, 41% strand	P00722

Ligands and binding sites

PTQ · 2-phenylethyl 1-thio-beta-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
NA · Sodium ion · metal · 8 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1183	0.82	0.84	114	empty
2	595	0.80	0.86	74	empty
3	1123	0.76	0.78	105	empty
4	1174	0.75	0.78	106	empty
5	1142	0.75	0.77	104	empty

Interfaces

6 interfaces between chains.

B–C · 2560 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 2558 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 2109 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 2108 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 111 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6CVM · Atomic resolution cryo-EM structure of beta-galactosidase · 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 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 P00722
Elsewhere: RCSB PDB 6CVM · PDBe 6CVM · UniProt P00722

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