MolNFT v1 · #92842 · protein

Crystal structure of a carbohydrate-binding domain

4GKX · Protein ergic-53: “Crystal structure of a carbohydrate-binding domain”. X-ray diffraction, 2 ligands (MAN, CA), 9 pockets (best druggability 0.76). MolNFT v1 #92842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GKX
Type: protein
Length: 1,380 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein ergic-53
UniProt: P49257
Ligands: MAN, CA
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Protein ergic-53	protein	230	3% helix, 47% strand	P49257

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B, C, D, E, F
CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 7 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	852	0.76	0.80	69	empty
2	777	0.73	0.79	60	empty
3	689	0.73	0.79	49	empty
4	371	0.58	0.76	45	empty
5	223	0.51	0.76	35	empty

Interfaces

5 interfaces between chains.

C–E · 631 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 619 Å² buried · 6 hydrogen bonds · protein-protein
D–F · 453 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 414 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 413 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4GKX · Crystal structure of a carbohydrate-binding domain · the same entry in another collection · chain C against C, TM-score 1.00
P49257 · AlphaFold monomer V2.0 prediction for protein ergic-53 (P49257) · 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 P49257
Elsewhere: RCSB PDB 4GKX · PDBe 4GKX · UniProt P49257

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