MolNFT v1 · #63085 · protein

PFA1 Fab fragment complexed with ROR2(518-525)

3EYU · If kappa light chain: “PFA1 Fab fragment complexed with ROR2(518-525)”. X-ray diffraction, 4 pockets (best druggability 0.50). MolNFT v1 #63085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EYU
Type: protein
Length: 444 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: If kappa light chain; PFA1 Fab heavy chain; ROR2(518-525) peptide
UniProt: A2NHM3
Pockets: 4 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	If kappa light chain	protein	219	7% helix, 50% strand	A2NHM3
H	PFA1 Fab heavy chain	protein	219	5% helix, 46% strand	—
Q	ROR2(518-525) peptide	protein	6	0% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	286	0.50	0.73	37	empty
2	80	0.35	0.76	18	empty
3	80	0.33	0.74	18	empty
4	79	0.29	0.72	19	empty

Interfaces

3 interfaces between chains.

L–H · 1897 Å² buried · 19 hydrogen bonds · protein-protein
H–Q · 351 Å² buried · 9 hydrogen bonds · protein-protein
L–Q · 340 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 modified (disulfide, alkylation).

Compared structures

3EYU · PFA1 Fab fragment complexed with Ror2(518-525) · the same entry in another collection · chain L against L, 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 A2NHM3
Elsewhere: RCSB PDB 3EYU · PDBe 3EYU · UniProt A2NHM3

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