MolNFT v1 · #91105 · protein

Crystal structure of MSLN7-64 morab-009 Fab complex

4F3F · Morab-009 Fab light chain: “Crystal structure of MSLN7-64 morab-009 Fab complex”. X-ray diffraction, 4 pockets (best druggability 0.65). MolNFT v1 #91105 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4F3F
Type: protein
Length: 490 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Morab-009 Fab light chain; Morab-009 Fab heavy chain; Mesothelin
UniProt: Q13421
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Morab-009 Fab light chain	protein	211	6% helix, 52% strand	—
B	Morab-009 Fab heavy chain	protein	220	10% helix, 52% strand	—
C	Mesothelin	protein	59	63% helix, 0% strand	Q13421

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	656	0.65	0.75	60	empty
2	150	0.42	0.75	22	empty
3	80	0.32	0.74	21	empty
4	62	0.29	0.74	16	empty

Interfaces

3 interfaces between chains.

A–B · 1831 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 626 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 390 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).

Compared structures

4F3F · Crystal Structure of Msln7-64 MORAb-009 FAB complex · the same entry in another collection · chain A against A, TM-score 1.00
Q13421 · AlphaFold monomer V2.0 prediction for mesothelin (Q13421) · a predicted model of the same protein · chain C 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 Q13421
Elsewhere: RCSB PDB 4F3F · PDBe 4F3F · UniProt Q13421

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