MolNFT v1 · #102141 · protein

Fab for methotrexate (unbound apo)

4OCY · Fab ADD058 heavy chain: “Fab for methotrexate (unbound apo)”. X-ray diffraction, 3 pockets (best druggability 0.70). MolNFT v1 #102141 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OCY
Type: protein
Length: 426 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab ADD058 heavy chain; Fab ADD058 light chain
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab ADD058 heavy chain	protein	210	4% helix, 53% strand	—
L	Fab ADD058 light chain	protein	216	6% helix, 51% strand	—

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	168	0.70	0.88	30	empty
2	317	0.52	0.74	48	empty
3	127	0.41	0.75	26	empty

Interfaces

1 interface between chains.

H–L · 1806 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4OCY · Fab for methotrexate (unbound apo) · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 4OCY · PDBe 4OCY

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