1LDP

CRYSTAL STRUCTURE OF MURINE MHC CLASS I H-2LD WITH A MIXTURE OF BOUND PEPTIDES

• PDB DOI: https://doi.org/10.2210/pdb1LDP/pdb

• Classification: COMPLEX (MHC I/PEPTIDE)
• Organism(s): Mus musculus, Drosophila melanogaster
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 1998-03-15 Released: 1998-06-17 
• Deposition Author(s): Speir, J.A., Wilson, I.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.371 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.55 kDa 
• Atom Count: 3,205 
• Modelled Residue Count: 389 
• Deposited Residue Count: 389 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS I H-2LD	A [auth H]	272	Mus musculus	Mutation(s): 0  Gene Names: H-2LD
UniProt
Find proteins for P01897 (Mus musculus) Explore P01897  Go to UniProtKB:  P01897

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS I H-2LD	B [auth L]	99	Mus musculus	Mutation(s): 0  Gene Names: H-2LD
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE	C [auth P]	9	Drosophila melanogaster	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE	D [auth Q]	9	Drosophila melanogaster	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.371 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.4	α = 90
b = 48.98	β = 97.95
c = 84.06	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-17 
Deposition Author(s): Speir, J.A., Wilson, I.A.

Revision History  

• Version 1.0: 1998-06-17
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-09
  Changes: Database references, Refinement description, Structure summary