3D2U
Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor
- PDB DOI: https://doi.org/10.2210/pdb3D2U/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Human betaherpesvirus 5, Homo sapiens
- Mutation(s): Yes 
- Deposited: 2008-05-08 Released: 2008-07-08 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.21 Å
- R-Value Free: 0.259 
- R-Value Work: 0.241 
This is version 1.6 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 |
UL18 protein | A, D [auth E] | 281 | Human betaherpesvirus 5 | Mutation(s): 5  | |
UniProt | |||||
Find proteins for P08560 (Human cytomegalovirus (strain AD169)) Explore P08560  Go to UniProtKB:  P08560 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P08560 | ||||
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 |
Beta-2-microglobulin | B, E [auth F] | 99 | Homo sapiens | Mutation(s): 3  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769 | |||||
PHAROS:  P61769 GTEx:  ENSG00000166710  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Leukocyte immunoglobulin-like receptor subfamily B member 1 | C [auth D], F [auth H] | 198 | Homo sapiens | Mutation(s): 3  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q8NHL6 (Homo sapiens) Explore Q8NHL6  Go to UniProtKB:  Q8NHL6 | |||||
PHAROS:  Q8NHL6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q8NHL6 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Actin | G, H [auth C] | 9 | Homo sapiens | Mutation(s): 5  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P60709 (Homo sapiens) Explore P60709  Go to UniProtKB:  P60709 | |||||
PHAROS:  P60709 GTEx:  ENSG00000075624  | |||||
Entity Groups   | |||||
UniProt Group | P60709 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | I [auth A] J [auth A] N [auth A] O [auth A] P [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
BMA Query on BMA | L [auth A] | beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N | |||
MAN Query on MAN | K [auth A] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N | |||
FUC Query on FUC | M [auth A] | alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.21 Å
- R-Value Free: 0.259 
- R-Value Work: 0.241 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 52.366 | α = 90 |
b = 98.11 | β = 98.46 |
c = 172.147 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
DM | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
Entry History 
Deposition Data
- Released Date: 2008-07-08  Deposition Author(s): Yang, Z., Bjorkman, P.J.
Revision History (Full details and data files)
- Version 1.0: 2008-07-08
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2017-10-25
Changes: Advisory, Refinement description - Version 1.3: 2019-12-25
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2021-10-20
Changes: Advisory, Database references, Structure summary - Version 1.6: 2023-08-30
Changes: Data collection, Refinement description