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FGFR4 D2 - Fab complex

Analyse FGFR4 D2 - Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6J6Y
Type: protein
Length: 1,061 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibroblast growth factor receptor 4; Fab heavy chain; Fab light chain
EC: 2.7.10.1
UniProt: P22455
Pockets: 10 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibroblast growth factor receptor 4 (EC 2.7.10.1)	protein	101	7% helix, 51% strand	P22455
B	Fab heavy chain	protein	215	10% helix, 52% strand	—
C	Fab light chain	protein	215	9% helix, 52% strand	—
D	Fibroblast growth factor receptor 4 (EC 2.7.10.1)	protein	101	10% helix, 52% strand	P22455
E	Fab heavy chain	protein	216	7% helix, 51% strand	—
F	Fab light chain	protein	213	6% helix, 52% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1011	0.70	0.75	97	empty
2	332	0.59	0.77	44	empty
3	366	0.57	0.75	39	empty
4	210	0.51	0.76	28	empty
5	199	0.49	0.76	41	empty

Interfaces

9 interfaces between chains.

B–C · 1640 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1620 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 991 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 527 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 494 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6J6Y · FGFR4 D2 - Fab complex · the same entry in another collection · chain F against F, TM-score 1.00
P22455 · AlphaFold monomer V2.0 prediction for fibroblast growth factor receptor 4 (P22455) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 P22455
Elsewhere: RCSB PDB 6J6Y · PDBe 6J6Y · UniProt P22455

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