5EZI
Crystal Structure of Fab of parasite invasion inhibitory antibody c1 - hexagonal form
- PDB DOI: https://doi.org/10.2210/pdb5EZI/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2015-11-26 Released: 2017-01-25 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.61 Å
- R-Value Free: 0.221 
- R-Value Work: 0.195 
- R-Value Observed: 0.196 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fab c12 heavy chain | A [auth H] | 222 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fab c12 Light chain | B [auth L] | 214 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | C [auth A] | 9 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G58667NI GlyCosmos:  G58667NI GlyGen:  G58667NI |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CL Query on CL | D [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.61 Å
- R-Value Free: 0.221 
- R-Value Work: 0.195 
- R-Value Observed: 0.196 
- Space Group: P 65 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 82.7 | α = 90 |
b = 82.7 | β = 90 |
c = 361.88 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2017-01-25  Deposition Author(s): Favuzza, P., Pluschke, G., Rudolph, M.G.
Revision History (Full details and data files)
- Version 1.0: 2017-01-25
Type: Initial release - Version 1.1: 2017-02-15
Changes: Structure summary - Version 1.2: 2017-03-01
Changes: Structure summary - Version 1.3: 2017-04-26
Changes: Other, Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary