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Crystal structure analysis of FGF1-DISACCHARIDE(NI24) complex

Analyse Crystal structure analysis of FGF1-DISACCHARIDE(NI24) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UDA
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heparin-binding growth factor 1
UniProt: P05230
Ligands: IDY, SUS, PO4
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparin-binding growth factor 1	protein	126	12% helix, 42% strand	P05230
B	Heparin-binding growth factor 1	protein	127	9% helix, 43% strand	P05230
C	Heparin-binding growth factor 1	protein	129	9% helix, 40% strand	P05230

Ligands and binding sites

IDY · 1-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid · ligand · chains B
SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · chains B
PO4 · Phosphate ion · ion · 3 copies · chains C

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

Pockets

3 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	86	0.43	0.80	16	empty
2	141	0.41	0.74	26	empty
3	65	0.34	0.77	14	empty

Interfaces

2 interfaces between chains.

B–C · 572 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 399 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3UDA · Crystal Structure Analysis of FGF1-Disaccharide(NI24) 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 C against A, TM-score 0.98

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 3UDA · PDBe 3UDA · UniProt P05230

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