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Crystal Structure Analysis of FGF1-Disaccharide(NI23) complex

Analyse Crystal Structure Analysis of FGF1-Disaccharide(NI23) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UD9
Type: protein
Length: 383 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.34
Source: Homo sapiens
Molecule: Heparin-binding growth factor 1
UniProt: P05230
Ligands: IDY, SGN, PO4
Pockets: 4 · best druggability 0.48

Structure

x-ray diffraction · resolution 2.34 · 3 distinct chains · 9% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparin-binding growth factor 1	protein	128	9% helix, 43% strand	P05230
B	Heparin-binding growth factor 1	protein	128	9% helix, 41% strand	P05230
C	Heparin-binding growth factor 1	protein	127	7% helix, 39% strand	P05230

Ligands and binding sites

IDY · 1-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains B
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains B
PO4 · Phosphate ion · ion · 4 copies · chains A, C

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	170	0.48	0.76	26	empty
2	77	0.34	0.75	24	empty
3	51	0.30	0.76	13	PO4
4	63	0.27	0.73	17	empty

Interfaces

2 interfaces between chains.

A–B · 553 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 408 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3UD9 · Crystal structure analysis of FGF1-DISACCHARIDE(NI23) complex · the same entry in another collection · chain A against A, TM-score 1.00
P05230 · AlphaFold monomer V2.0 prediction for fibroblast growth factor 1 (P05230) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P05230
Elsewhere: RCSB PDB 3UD9 · PDBe 3UD9 · UniProt P05230

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