7C94

Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide

• PDB DOI: https://doi.org/10.2210/pdb7C94/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-04 Released: 2020-09-30 
• Deposition Author(s): Suzuki, K., Nakamura, S., Ogasawara, S., Naruchi, K., Shimabukuro, J., Tukahara, N., Kaneko, M.K., Kato, Y., Murata, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.255 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.54 kDa 
• Atom Count: 7,077 
• Modelled Residue Count: 901 
• Deposited Residue Count: 926 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab fragment	A, D	220	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab fragment	B, E	225	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Podoplanin	C, F	18	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q86YL7 (Homo sapiens) Explore Q86YL7  Go to UniProtKB:  Q86YL7
PHAROS:  Q86YL7 GTEx:  ENSG00000162493

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose	G, H	4		O-Glycosylation
Glycosylation Resources
GlyTouCan:  G01614ZM GlyCosmos:  G01614ZM GlyGen:  G01614ZM

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth A], N [auth D], O [auth D], S [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	J [auth A], K [auth A], L [auth B], M [auth B], P [auth D], Q [auth D], R [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.255 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.1	α = 90
b = 42.96	β = 91.366
c = 221.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Suzuki, K., Nakamura, S., Ogasawara, S., Naruchi, K., Shimabukuro, J., Tukahara, N., Kaneko, M.K., Kato, Y., Murata, T.

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description