Research workbench

Meditope-enabled trastuzumab

Analyse Meditope-enabled trastuzumab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HJG
Type: protein
Length: 551 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trastuzumab light chain; Trastuzumab heavy chain; Immunoglobulin G-binding protein a…
UniProt: P0A015
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trastuzumab light chain	protein	214	6% helix, 51% strand	—
B	Trastuzumab heavy chain	protein	221	10% helix, 52% strand	—
H	Immunoglobulin G-binding protein a	protein	54	78% helix, 0% strand	P0A015
E	Protein L fragment	protein	62	35% helix, 45% strand	—

Pockets

5 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	641	0.64	0.74	71	empty
2	185	0.49	0.76	27	empty
3	131	0.49	0.79	33	empty
4	71	0.32	0.75	19	empty
5	60	0.28	0.74	18	empty

Interfaces

3 interfaces between chains.

A–B · 1942 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 706 Å² buried · 13 hydrogen bonds · protein-protein
B–H · 593 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4HJG · Meditope-enabled trastuzumab · the same entry in another collection · chain A against A, TM-score 1.00
P0A015 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P0A015) · a predicted model of the same protein · chain H against A, TM-score 0.89

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 P0A015
Elsewhere: RCSB PDB 4HJG · PDBe 4HJG · UniProt P0A015

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