9EJD | pdb_00009ejd

Crystal structure of HLA-B*07:02 with the 9-mer TP53 mutant peptide SPILTIITL

PDB DOI: https://doi.org/10.2210/pdb9EJD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-11-27 Released: 2026-06-24
Deposition Author(s): Tan, K., Mallis, R.J., Reinherz, E.L.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.267 (Depositor), 0.268 (DCC)
R-Value Work:
0.233 (Depositor), 0.233 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of HLA-B*07:02 with the 9-mer TP53 mutant peptide SPILTIITL

Tan, K., Mallis, R.J., Reinherz, E.L.

To be published.

Macromolecule Content

Total Structure Weight: 92.7 kDa
Atom Count: 6,640
Modeled Residue Count: 770
Deposited Residue Count: 772
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B alpha chain	A, D	277	Homo sapiens	Mutation(s): 0 Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889 Go to UniProtKB: P01889
PHAROS: P01889 GTEx: ENSG00000234745
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01889
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Cellular tumor antigen p53	C, F	9	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637 Go to UniProtKB: P04637
PHAROS: P04637 GTEx: ENSG00000141510
Entity Groups
UniProt Group	P04637
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] J [auth A] K [auth A] L [auth A] NA [auth E] AA [auth D], J [auth A], K [auth A], L [auth A], NA [auth E], OA [auth E], PA [auth E], Q [auth B], QA [auth E], R [auth B], S [auth B], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth D] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain TA [auth E] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth D]	G [auth A] H [auth A] I [auth A] IA [auth D] JA [auth D] G [auth A], H [auth A], I [auth A], IA [auth D], JA [auth D], KA [auth D], LA [auth D], MA [auth D], O [auth A], P [auth B], TA [auth E], V [auth B], W [auth B], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain O [auth A] Focus chain P [auth B] Focus chain TA [auth E] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain O [auth A] Focus chain P [auth B] Focus chain TA [auth E] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth D]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain N [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain N [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain N [auth A]	HA [auth D], N [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain N [auth A] Interactions & Density Focus chain HA [auth D] Focus chain N [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain M [auth A] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], M [auth A], RA [auth E], SA [auth E], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain M [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain M [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.267 (Depositor), 0.268 (DCC)
R-Value Work: 0.233 (Depositor), 0.233 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.432	α = 90
b = 64.547	β = 90
c = 83.975	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Tan, K.

Mallis, R.J.

Reinherz, E.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA265928
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01AI143565
National Institutes of Health/Office of the Director	United States	S10OD030394