6CPR

Crystal structure of 4-1BBL/4-1BB complex in C2 space group

PDB DOI: https://doi.org/10.2210/pdb6CPR/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Insect cell expression vector pTIE1
Mutation(s): No

Deposited: 2018-03-14 Released: 2018-05-09
Deposition Author(s): Aruna, B., Zajonc, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.280
R-Value Work: 0.249
R-Value Observed: 0.250

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 98.77 kDa
Atom Count: 6,257
Modelled Residue Count: 848
Deposited Residue Count: 909
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 9	A, B, C	165	Homo sapiens	Mutation(s): 0 Gene Names: TNFSF9
UniProt & NIH Common Fund Data Resources
Find proteins for P41273 (Homo sapiens) Explore P41273 Go to UniProtKB: P41273
PHAROS: P41273 GTEx: ENSG00000125657
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41273
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 9	D, E [auth F], F [auth E]	138	Homo sapiens	Mutation(s): 0 Gene Names: TNFRSF9, CD137, ILA
UniProt & NIH Common Fund Data Resources
Find proteins for Q07011 (Homo sapiens) Explore Q07011 Go to UniProtKB: Q07011
PHAROS: Q07011 GTEx: ENSG00000049249
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q07011
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain V [auth F] SDF format, chain W [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain V [auth F] MOL2 format, chain W [auth E]	Q [auth D], V [auth F], W [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth D] Focus chain V [auth F] Focus chain W [auth E] Interactions & Density Focus chain Q [auth D] Focus chain V [auth F] Focus chain W [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D]	J [auth A] K [auth A] N [auth B] P [auth C] S [auth D] J [auth A], K [auth A], N [auth B], P [auth C], S [auth D], T [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain X [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain X [auth E]	H [auth A] I [auth A] L [auth B] M [auth B] O [auth C] H [auth A], I [auth A], L [auth B], M [auth B], O [auth C], R [auth D], X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain X [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E]	U [auth D], Y [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain U [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.280
R-Value Work: 0.249
R-Value Observed: 0.250
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.28	α = 90
b = 66.504	β = 103.09
c = 129.356	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

Aruna, B.

Zajonc, D.M.

Revision History (Full details and data files)

Version 1.0: 2018-05-09
Type: Initial release
Version 1.1: 2018-07-11
Changes: Data collection, Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

6CPR

Crystal structure of 4-1BBL/4-1BB complex in C2 space group

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2