5MGT

Complex of human NKR-P1 and LLT1 in deglycosylated forms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of human NKR-P1:LLT1 receptor complex

Blaha, J.Skalova, T.Vanek, O.Stransky, J.Koval, T.Hasek, J.Yuguang, Z.Harlos, K.Dohnalek, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-type lectin domain family 2 member DA, B135Homo sapiensMutation(s): 1 
Gene Names: CLEC2DCLAXLLT1OCIL
Find proteins for Q9UHP7 (Homo sapiens)
Explore Q9UHP7 
Go to UniProtKB:  Q9UHP7
NIH Common Fund Data Resources
PHAROS:  Q9UHP7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Killer cell lectin-like receptor subfamily B member 1C, D, E, F146Homo sapiensMutation(s): 0 
Gene Names: KLRB1CLEC5BNKRP1A
Find proteins for Q12918 (Homo sapiens)
Explore Q12918 
Go to UniProtKB:  Q12918
NIH Common Fund Data Resources
PHAROS:  Q12918
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , K [auth B] , L [auth B] , O [auth C] , P [auth C] , R [auth D] , S [auth D] , 
G [auth A],  H [auth A],  K [auth B],  L [auth B],  O [auth C],  P [auth C],  R [auth D],  S [auth D],  V [auth E],  W [auth F],  X [auth F],  Y [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], M [auth B], N [auth B], Q [auth C], T [auth D], Z [auth F]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
U [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.58α = 90
b = 80.15β = 90
c = 272.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic15-15181S
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLG14009

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary