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
Deposition Author(s): Zajonc, D.M., Bitra, A.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 67.39 kDa
Atom Count: 4,333
Modelled Residue Count: 539
Deposited Residue Count: 572
Unique protein chains: 1

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	A, B, C, D	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 Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	Interactions Focus chain E Interactions & Density Focus chain E
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	Interactions Focus chain F Focus chain H Interactions & Density Focus chain F Focus chain H
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	Interactions Focus chain G Interactions & Density Focus chain G
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 Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B]	S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], T [auth B], V [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain Z [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	N [auth A] P [auth B] Q [auth B] R [auth B] U [auth C] N [auth A], P [auth B], Q [auth B], R [auth B], U [auth C], W [auth D], X [auth D], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

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 Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

5WI8

Crystal structure of murine 4-1BB from HEK293T cells in P21 space group

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)