7NMD

Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL

PDB DOI: https://doi.org/10.2210/pdb7NMD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-02-23 Released: 2022-09-07
Deposition Author(s): Rizkallah, P.J., Sewell, A.K., Cole, D.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7NME 7NMF 7NMG

Literature

Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL

Rizkallahp, P.J., Sewell, A.K., Cole, D.K.

To be published.

Macromolecule Content

Total Structure Weight: 91.22 kDa
Atom Count: 6,657
Modelled Residue Count: 770
Deposited Residue Count: 770
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt
Find proteins for A0A5H2UYS3 (Homo sapiens) Explore A0A5H2UYS3 Go to UniProtKB: A0A5H2UYS3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5H2UYS3
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human MHC Class I, beta 2 microglobulin	B, E	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU	C, F	9	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	H [auth A] I [auth A] P [auth B] Q [auth B] U [auth D] H [auth A], I [auth A], P [auth B], Q [auth B], U [auth D], Y [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth D] Focus chain Y [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain V [auth D] SDF format, chain Z [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth F]	J [auth A] K [auth A] L [auth A] R [auth B] V [auth D] J [auth A], K [auth A], L [auth A], R [auth B], V [auth D], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain V [auth D] Focus chain Z [auth F] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain V [auth D] Focus chain Z [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain X [auth E] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E]	G [auth A] M [auth B] N [auth B] O [auth B] S [auth D] G [auth A], M [auth B], N [auth B], O [auth B], S [auth D], T [auth D], W [auth E], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth D] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth D] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth E]