6MI2

Structure of the human 4-1BB / Utomilumab Fab complex

PDB DOI: https://doi.org/10.2210/pdb6MI2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens, Trichoplusia ni
Mutation(s): No

Deposited: 2018-09-19 Released: 2018-11-21
Deposition Author(s): Kimberlin, C.R., Chin, S.M., Roe-Zurz, Z., Xu, A., Yang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.278
R-Value Work: 0.238
R-Value Observed: 0.240

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: 129.7 kDa
Atom Count: 8,119
Modelled Residue Count: 1,115
Deposited Residue Count: 1,178
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Utomilumab Fab heavy chain	A, C [auth D]	230	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Utomilumab Fab lambda chain	B, D [auth E]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 9	E [auth F], F [auth C]	145	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

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

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 BA [auth C] MOL2 format, chain BA [auth C]	BA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth C] Interactions & Density Focus chain BA [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F]	AA [auth F] CA [auth C] DA [auth C] EA [auth C] FA [auth C] AA [auth F], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], T [auth D], U [auth D], V [auth E], W [auth E], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E]	IA [auth C] JA [auth C] K [auth A] KA [auth C] Q [auth B] IA [auth C], JA [auth C], K [auth A], KA [auth C], Q [auth B], R [auth B], S [auth B], X [auth E], Y [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth E] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.278
R-Value Work: 0.238
R-Value Observed: 0.240
Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.903	α = 90
b = 73.338	β = 98.99
c = 175.121	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary