MolNFT v1 · #4469 · protein

E. COLI beta-galactosidase at 1.7 ångström

1DP0: “E. COLI beta-galactosidase at 1.7 ångström”. X-ray diffraction, 2 ligands (NA, MG), 20 pockets (best druggability 0.81). MolNFT v1 #4469 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DP0
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: NA, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 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	1011	14% helix, 41% strand	P00722

Ligands and binding sites

NA · Sodium ion · metal · 20 copies · chains A, B, C, D
MG · Magnesium ion · metal · 16 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 112 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	915	0.81	0.83	113	empty
2	745	0.79	0.83	104	DMS
3	588	0.76	0.83	64	empty
4	51	0.72	1.00	20	empty
5	50	0.71	0.99	19	empty

Interfaces

6 interfaces between chains.

B–C · 2360 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 2341 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 2025 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 2011 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 140 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1DP0 · E. COLI beta-galactosidase at 1.7 ångström · 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 1DP0 · PDBe 1DP0 · UniProt P00722

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