5L7X
Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II
- PDB DOI: https://doi.org/10.2210/pdb5L7X/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No 
- Deposited: 2016-06-04 Released: 2016-07-13 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.228 
- R-Value Work: 0.190 
- R-Value Observed: 0.192 
This is version 1.5 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 |
Mouse Antibody Fab Fragment, IgG1-kappa Heavy Chain | A [auth H] | 220 | Mus musculus | 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 |
Mouse Antibody Fab Fragment, IgG1-kappa Light Chain | B [auth L] | 215 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
1PE Query on 1PE | G [auth L] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N | |||
NAG Query on NAG | H [auth L] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PG4 Query on PG4 | C [auth H] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N | |||
PEG Query on PEG | D [auth H], E [auth H], F [auth H] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.228 
- R-Value Work: 0.190 
- R-Value Observed: 0.192 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 67.491 | α = 90 |
b = 72.196 | β = 90 |
c = 88.941 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
Aimless | data scaling |
autoPROC | data reduction |
BALBES | phasing |
Entry History 
Deposition Data
- Released Date: 2016-07-13  Deposition Author(s): Rupp, B., Naschberger, A.
Revision History (Full details and data files)
- Version 1.0: 2016-07-13
Type: Initial release - Version 1.1: 2016-12-07
Changes: Database references - Version 1.2: 2016-12-21
Changes: Database references - Version 1.3: 2018-01-31
Changes: Database references - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary - Version 1.5: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary