Research workbench

Trastuzumab Fab V3

Analyse Trastuzumab Fab V3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B9Z
Type: protein
Length: 552 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trastuzumab Fab light chain; Trastuzumab Fab heavy chain; Protein L; Immunoglobulin G…
UniProt: P01834, S6B291, Q51918, Q2UW42
Pockets: 5 · best druggability 0.65

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trastuzumab Fab light chain	protein	214	6% helix, 51% strand	P01834
B	Trastuzumab Fab heavy chain	protein	221	10% helix, 52% strand	S6B291
E	Protein L	protein	63	35% helix, 44% strand	Q51918
C	Immunoglobulin G binding protein a	protein	54	78% helix, 0% strand	Q2UW42

Pockets

5 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	658	0.65	0.75	73	empty
2	184	0.56	0.80	29	empty
3	96	0.41	0.77	24	empty
4	75	0.33	0.75	19	empty
5	61	0.27	0.73	17	empty

Interfaces

3 interfaces between chains.

A–B · 1994 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 733 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 610 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, oxidation).

Compared structures

6B9Z · Trastuzumab Fab v3 · the same entry in another collection · chain A against A, TM-score 1.00
P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain A against A, TM-score 0.50

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 P01834
Every structure of UniProt S6B291
Every structure of UniProt Q51918
Every structure of UniProt Q2UW42
Elsewhere: RCSB PDB 6B9Z · PDBe 6B9Z · UniProt P01834 · UniProt S6B291 · UniProt Q51918 · UniProt Q2UW42

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