Research workbench

Meditope enabled trastuzumab I83E variant in complex with (ac) CQFDA(PH)2STRRLRCGGSK

Analyse Meditope enabled trastuzumab I83E variant in complex with (ac)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U5F
Type: protein
Length: 567 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Memab trastuzumab Fab light chain I83E; Memab trastuzumab Fab heavy chain; Protein L…
UniProt: Q51918, Q2UW42
Ligands: MRY
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 5 distinct chains · 17% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Memab trastuzumab Fab light chain I83E	protein	214	6% helix, 51% strand	—
B	Memab trastuzumab Fab heavy chain	protein	223	9% helix, 53% strand	—
E	Protein L	protein	63	35% helix, 44% strand	Q51918
D	5-diphenyl long meditope	protein	13	0% helix, 46% strand	—
C	Immunoglobulin G binding protein a	protein	54	78% helix, 0% strand	Q2UW42

Ligands and binding sites

MRY · Meso-erythritol · ligand · chains B, D

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.65	0.96	17	empty
2	410	0.61	0.76	47	MRY
3	179	0.56	0.80	29	empty
4	312	0.55	0.75	48	empty
5	255	0.51	0.75	43	empty

Interfaces

6 interfaces between chains.

A–B · 2020 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 710 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 601 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 512 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 491 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5U5F · MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT IN COMPLEX WITH (Ac) CQFDA(PH)2STRRLRCGGSK · the same entry in another collection · chain A against A, 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
Every structure of UniProt Q51918
Every structure of UniProt Q2UW42
Elsewhere: RCSB PDB 5U5F · PDBe 5U5F · UniProt Q51918 · UniProt Q2UW42

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.