5WI8
Crystal structure of murine 4-1BB from HEK293T cells in P21 space group
- PDB DOI: https://doi.org/10.2210/pdb5WI8/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Mammalian expression vector pcDNA3-N-HA-LIC
- Mutation(s): No 
- Deposited: 2017-07-18 Released: 2017-12-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.95 Å
- R-Value Free: 0.279 
- R-Value Work: 0.235 
- R-Value Observed: 0.238 
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 |
Tumor necrosis factor receptor superfamily member 9 | 143 | Mus musculus | Mutation(s): 0  Gene Names: Tnfrsf9, Cd137, Ila, Ly63 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P20334 (Mus musculus) Explore P20334  Go to UniProtKB:  P20334 | |||||
IMPC:  MGI:1101059 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P20334 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | E | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | F, H | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G00395TQ GlyCosmos:  G00395TQ GlyGen:  G00395TQ |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | S [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
EDO Query on EDO | N [auth A] P [auth B] Q [auth B] R [auth B] U [auth C] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.95 Å
- R-Value Free: 0.279 
- R-Value Work: 0.235 
- R-Value Observed: 0.238 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 65.011 | α = 90 |
b = 61.763 | β = 91.53 |
c = 110.75 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2017-12-20  Deposition Author(s): Zajonc, D.M., Bitra, A.
Revision History (Full details and data files)
- Version 1.0: 2017-12-20
Type: Initial release - Version 1.1: 2018-10-31
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary