6H6D

Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with adenovirus-derived peptide Ad10

PDB DOI: https://doi.org/10.2210/pdb6H6D/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, unidentified adenovirus
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2018-07-27 Released: 2019-08-14
Deposition Author(s): Achour, A., Sandalova, T., Han, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.233
R-Value Work: 0.198
R-Value Observed: 0.200

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of H-2Db and H-2Dbm13 with cancer-associated Ad 10 peptide reveal that subtle changes in the peptide environment impact thermostability and alloreactivity

Han, X., Abualrous, E.T., Badia-Martines, D., Sandalova, T., Sun, R., van Hall, T., Ossendorp, F., Achour, A.

To be published.

Macromolecule Content

Total Structure Weight: 103.81 kDa
Atom Count: 6,479
Modelled Residue Count: 763
Deposited Residue Count: 894
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, D-B alpha chain	A, D	338	Mus musculus	Mutation(s): 0 Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus) Explore P01899 Go to UniProtKB: P01899
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01899
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	99	Mus musculus	Mutation(s): 1 Gene Names: B2m
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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Early E1A protein	C, F	10	unidentified adenovirus	Mutation(s): 0
UniProt
Find proteins for P03255 (Human adenovirus C serotype 5) Explore P03255 Go to UniProtKB: P03255
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03255
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain Y [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth E]	G [auth A], H [auth A], P [auth B], Y [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Y [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	AA [auth E] I [auth A] J [auth A] K [auth A] Q [auth B] AA [auth E], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], V [auth D], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth D] Focus chain Z [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	BA [auth E] CA [auth E] L [auth A] M [auth A] N [auth A] BA [auth E], CA [auth E], L [auth A], M [auth A], N [auth A], O [auth A], S [auth B], T [auth B], U [auth B], W [auth D], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth D] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.233
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.14	α = 84.2
b = 69.24	β = 86.69
c = 87.16	γ = 81.75

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Achour, A.

Sandalova, T.

Han, X.

Revision History (Full details and data files)

Version 1.0: 2019-08-14
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary