1FZM

MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN

PDB DOI: https://doi.org/10.2210/pdb1FZM/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Vesicular stomatitis Indiana virus (strain Glasgow)
Expression System: Drosophila melanogaster
Mutation(s): Yes

Deposited: 2000-10-03 Released: 2001-03-28
Deposition Author(s): Rudolph, M.G., Speir, J.A., Brunmark, A., Mattsson, N., Jackson, M.R., Peterson, P.A., Teyton, L., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223
R-Value Work: 0.210
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 45.58 kDa
Atom Count: 3,540
Modelled Residue Count: 381
Deposited Residue Count: 381
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN	A	274	Mus musculus	Mutation(s): 5
UniProt
Find proteins for P01901 (Mus musculus) Explore P01901 Go to UniProtKB: P01901
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01901
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (BETA-2-MICROGLOBULIN)	B	99	Mus musculus	Mutation(s): 0
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 Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (NUCLEOCAPSID PROTEIN)	C [auth P]	8	N/A	Mutation(s): 0
UniProt
Find proteins for P11212 (Vesicular stomatitis Indiana virus (strain Glasgow)) Explore P11212 Go to UniProtKB: P11212
Entity Groups
UniProt Group	P11212
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	3		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B]	H [auth A], J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B]	F [auth A], I [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223
R-Value Work: 0.210
R-Value Observed: 0.210
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.26	α = 90
b = 88.15	β = 90
c = 45.59	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2001-03-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-03-28
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2021-11-03
Changes: Database references, Structure summary