Macromolecule Content

Total Structure Weight: 26.89 kDa
Atom Count: 1966
Modelled Residue Count: 231
Deposited Residue Count: 250
Unique protein chains: 2

6TGG

scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar

DOI: 10.2210/pdb6TGG/pdb

Classification: ANTITUMOR PROTEIN
Organism(s): Mus musculus, Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2019-11-15 Released: 2020-04-08
Deposition Author(s): Bermejo, I.A., Navo, C.D., Castro-Lopez, J., Samchez-Fernandez, E.M., Guerreiro, A., Avenoza, A., Busto, J.H., Garcia-Martin, F., Nishimura, S.I., Garcia-Fernandez, J.M., Ortiz-Mellet, C., Bernardes, G.J.L., Hurtado-Guerrero, R., Peregrina, J.M., Corzana, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.237
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Synthesis, Conformational Analysis and in vivo Assays of an Anti-cancer Vaccine that features an Unnatural Antigen based on a sp2-Iminosugar Fragment

Corzana, F., Bermejo, I.A., Navo, C.D., Castro-Lopez, J., Guerreiro, A., Jimenez-Moreno, E., Sanchez-Fernandez, E.M., Garcia-Martin, F., Hinou, H., Nishimura, S.I., Garcia-Fernandez, J.M.M., Ortiz-Mellet, C., Avenoza, A., Busto, J.H., Bernardes, G.J.L., Hurtado-Guerrero, R., Peregrina, J.M.

(2020) Chem Sci

DOI: 10.1039/C9SC06334J

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ScFv_SM3	A [auth H]	244	Mus musculus	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-1	B [auth P]	6	Homo sapiens	Mutation(s): 0 Gene Names: MUC1, PUM
UniProt & NIH Common Fund Data Resources
Find proteins for P15941 (Homo sapiens) Explore P15941 Go to UniProtKB: P15941
PHAROS: P15941 GTEx: ENSG00000185499
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N8W Query on N8W Download Ideal Coordinates CCD File SDF format, chain G [auth P] MOL2 format, chain G [auth P]	G [auth P]	~{N}-[(6~{S},7~{R},8~{S},8~{a}~{R})-7,8-bis(oxidanyl)-3-oxidanylidene-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyridin-6-yl]ethanamide C₉ H₁₄ N₂ O₅ MKTHKMZBVDELIA-OSMVPFSASA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain F [auth H] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H]	C [auth H], D [auth H], E [auth H], F [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.237
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.271	α = 90
b = 68.689	β = 90
c = 90.393	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2019-11-15
Released Date: 2020-04-08

Deposition Author(s):

Castro-Lopez, J.

Samchez-Fernandez, E.M.

Garcia-Martin, F.

Nishimura, S.I.

Garcia-Fernandez, J.M.

Ortiz-Mellet, C.

Bernardes, G.J.L.

Hurtado-Guerrero, R.

Peregrina, J.M.

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.