MolNFT v1 · #143805 · protein

Trastuzumab Fab V3 in complex with cqfdlstrrlkc

6BAE · Trastuzumab Fab light chain: “Trastuzumab Fab V3 in complex with cqfdlstrrlkc”. X-ray diffraction, 2 ligands (ACE, NH2), 5 pockets (best druggability 0.65). MolNFT v1 #143805 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6BAE
Type: protein
Length: 566 residues
Chains: 5
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
Ligands: ACE, NH2
Pockets: 5 · best druggability 0.65

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trastuzumab Fab light chain	protein	214	5% helix, 51% strand	P01834
B	Trastuzumab Fab heavy chain	protein	223	11% helix, 53% strand	S6B291
E	Protein L	protein	63	35% helix, 41% strand	Q51918
C	Immunoglobulin G binding protein a	protein	54	78% helix, 0% strand	Q2UW42
D	Meditope	protein	12	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, E, D
NH2 · Amino group · ion · chains E, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	531	0.65	0.77	58	empty
2	213	0.54	0.78	28	empty
3	250	0.52	0.76	44	ACE
4	179	0.45	0.75	33	empty
5	92	0.42	0.78	22	empty

Interfaces

6 interfaces between chains.

A–B · 1934 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 738 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 603 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 501 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 411 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

6BAE · Trastuzumab Fab v3 in complex with CQFDLSTRRLKC · 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 6BAE · PDBe 6BAE · UniProt P01834 · UniProt S6B291 · UniProt Q51918 · UniProt Q2UW42

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