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 
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 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01897 | ||||
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 |
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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01887 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PEPTIDE | C [auth P] | 9 | Drosophila melanogaster | Mutation(s): 0  | |
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PEPTIDE | D [auth Q] | 9 | Drosophila melanogaster | Mutation(s): 0  | |
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on 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 Name | Purpose |
---|---|
XDS | data scaling |
SCALEPACK | data scaling |
X-PLOR | model building |
X-PLOR | refinement |
XDS | data reduction |
X-PLOR | phasing |
Entry History 
Deposition Data
- Released Date: 1998-06-17  Deposition Author(s): Speir, J.A., Wilson, I.A.
Revision History (Full details and data files)
- 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