MolNFT v1 · #102140 · protein

Fab complex with methotrexate

4OCX · Fab ADD056 heavy chain: “Fab complex with methotrexate”. X-ray diffraction, 1 ligand (MT1), 4 pockets (best druggability 0.66). MolNFT v1 #102140 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OCX
Type: protein
Length: 424 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab ADD056 heavy chain; Fab ADD056 light chain
Ligands: MT1
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab ADD056 heavy chain	protein	210	6% helix, 53% strand	—
L	Fab ADD056 light chain	protein	214	6% helix, 52% strand	—

Ligands and binding sites

MT1 · N-(4-{[(2,4-diaminopteridin-1-ium-6-yl)methyl](methyl)amino}benzoyl)-L-glutamic acid · ligand · chains H, L

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

Pockets

4 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	141	0.66	0.87	31	MT1
2	405	0.56	0.74	51	empty
3	113	0.39	0.75	25	empty
4	60	0.27	0.73	15	empty

Interfaces

1 interface between chains.

H–L · 1818 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4OCX · Fab complex with methotrexate · 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 4OCX · PDBe 4OCX

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