PDB Search results for query - Protein Data Bank Japan

PDB: 86 results

BlaR1 sensor domain from Staphylococcus aureus with N439V mutation
Descriptor:	GLYCEROL, Regulatory protein BlaR1, SULFATE ION
Authors:	Baker, B.M, Borbulevych, O.Y.
Deposit date:	2011-12-05
Release date:	2012-02-08
Last modified:	2024-02-28
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	An amino acid position at crossroads of evolution of protein function: antibiotic sensor domain of BlaR1 protein from Staphylococcus aureus versus clasS D beta-lactamases J.Biol.Chem., 287, 2012

8TBV

Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL
Descriptor:	Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, GLYCEROL, ...
Authors:	Arbuiso, A, Weiss, L.I, Brambley, C.A, Ma, J, Keller, G.L.J, Ayres, C.M, Baker, B.M.
Deposit date:	2023-06-29
Release date:	2024-01-17
Last modified:	2024-02-14
Method:	X-RAY DIFFRACTION (2.64 Å)
Cite:	Accurate modeling of peptide-MHC structures with AlphaFold. Structure, 32, 2024

8TBW

Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) peptide KLSHQPVLL
Descriptor:	Beta-2-microglobulin, HLA-A*02:01 alpha chain, NITRATE ION, ...
Authors:	Arbuiso, A, Weiss, L.I, Brambley, C.A, Ma, J, Keller, G.L.J, Ayres, C.M, Baker, B.M.
Deposit date:	2023-06-29
Release date:	2024-01-10
Last modified:	2024-02-14
Method:	X-RAY DIFFRACTION (2.081 Å)
Cite:	Accurate modeling of peptide-MHC structures with AlphaFold. Structure, 32, 2024

8U9G

Human Class I MHC HLA-A2 bound to sorting nexin 24 (127-135) neoantigen KLSHQLVLL
Descriptor:	2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, ...
Authors:	Arbuiso, A, Weiss, L.I, Brambley, C.A, Ma, J, Keller, G.L.J, Ayres, C.M, Baker, B.M.
Deposit date:	2023-09-19
Release date:	2024-01-10
Last modified:	2024-02-14
Method:	X-RAY DIFFRACTION (2.87 Å)
Cite:	Accurate modeling of peptide-MHC structures with AlphaFold. Structure, 32, 2024

7U21

Human Class I MHC HLA-A2 in complex with AVGSYVYSV peptide
Descriptor:	Beta-2-microglobulin, MHC class I antigen, A-2 alpha chain, ...
Authors:	Weiss, L.I, Baker, B.M.
Deposit date:	2022-02-22
Release date:	2022-06-01
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/MHC Complexes. Front Immunol, 13, 2022

8D5F

The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
Descriptor:	Beta-2-microglobulin, GLYCEROL, H-2 class I histocompatibility antigen, ...
Authors:	Custodio, J.M.F, Baker, B.M.
Deposit date:	2022-06-04
Release date:	2022-07-06
Last modified:	2024-01-17
Method:	X-RAY DIFFRACTION (2.31 Å)
Cite:	Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc.Natl.Acad.Sci.USA, 120, 2023

8D5E

The complex of Gtf2b Peptide TGAASFDEF Presented by H2-Dd
Descriptor:	Beta-2-microglobulin, GLYCEROL, H-2 class I histocompatibility antigen, ...
Authors:	Custodio, J.M.F, Baker, B.M.
Deposit date:	2022-06-04
Release date:	2022-07-06
Last modified:	2024-01-17
Method:	X-RAY DIFFRACTION (2.46 Å)
Cite:	Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc.Natl.Acad.Sci.USA, 120, 2023

8D5K

The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYLQVASHV Presented by H2-Kd
Descriptor:	Beta-2-microglobulin, H-2 class I histocompatibility antigen, K-D alpha chain, ...
Authors:	Custodio, J.M.F, Baker, B.M.
Deposit date:	2022-06-05
Release date:	2022-07-06
Last modified:	2024-01-17
Method:	X-RAY DIFFRACTION (2.066 Å)
Cite:	Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc.Natl.Acad.Sci.USA, 120, 2023

8D5J

The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd
Descriptor:	Beta-2-microglobulin, MHC class I heavy chain maturation peptide H-2K(D), Pre-mRNA-processing factor 19
Authors:	Custodio, J.M.F, Baker, B.M.
Deposit date:	2022-06-04
Release date:	2022-07-06
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.95 Å)
Cite:	The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd To Be Published

8FHL

Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd
Descriptor:	Beta-2-microglobulin, H-2 class I histocompatibility antigen, D-D alpha chain, ...
Authors:	Custodio, J.M.F, Baker, B.M.
Deposit date:	2022-12-14
Release date:	2023-06-28
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.194 Å)
Cite:	Structure of Pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd To Be Published

8FHU

Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by H2-Dd
Descriptor:	Beta-2-microglobulin, H-2 class I histocompatibility antigen, D-D alpha chain, ...
Authors:	Custodio, J.M.F, Baker, B.M.
Deposit date:	2022-12-15
Release date:	2023-06-28
Method:	X-RAY DIFFRACTION (1.801 Å)
Cite:	Structure of Pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd To Be Published

6VM7

SILv44 T cell receptor bound to HLA-A2 presenting gp100 peptide (ITDQVPFSV)
Descriptor:	Beta-2-microglobulin, GLYCEROL, MHC class I antigen, ...
Authors:	Smith, A.R, Baker, B.M.
Deposit date:	2020-01-27
Release date:	2021-01-20
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (2.41 Å)
Cite:	Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner Proc.Natl.Acad.Sci.USA, 118, 2021

6VMA

T4H2 T cell receptor bound to HLA-A2 presenting gp100 peptide (ITDQVPFSV)
Descriptor:	Beta-2-microglobulin, MHC class I antigen, A-2 alpha chain, ...
Authors:	Smith, A.R, Baker, B.M.
Deposit date:	2020-01-27
Release date:	2021-01-20
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (2.75 Å)
Cite:	Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner Proc.Natl.Acad.Sci.USA, 118, 2021

6VM9

T4H2 T cell receptor bound to HLA-A2 presenting gp100T2M peptide (IMDQVPFSV)
Descriptor:	Beta-2-microglobulin, MHC class I antigen, A-2 alpha chain, ...
Authors:	Smith, A.R, Baker, B.M.
Deposit date:	2020-01-27
Release date:	2021-01-20
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (2.9 Å)
Cite:	Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner Proc.Natl.Acad.Sci.USA, 118, 2021

6VMC

T4H2 T cell receptor bound to HLA-A2 presenting gp100T2L peptide (ILDQVPFSV)
Descriptor:	Beta-2-microglobulin, GLYCEROL, MHC class I antigen, ...
Authors:	Smith, A.R, Baker, B.M.
Deposit date:	2020-01-27
Release date:	2021-01-20
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (2.85 Å)
Cite:	Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner Proc.Natl.Acad.Sci.USA, 118, 2021

6VM8

SILv44 T cell receptor bound to HLA-A2 presenting gp100T2M peptide (IMDQVPFSV)
Descriptor:	Beta-2-microglobulin, CITRATE ANION, MHC class I antigen, ...
Authors:	Smith, A.R, Baker, B.M.
Deposit date:	2020-01-27
Release date:	2020-11-25
Last modified:	2021-06-09
Method:	X-RAY DIFFRACTION (2.41 Å)
Cite:	Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner. Proc.Natl.Acad.Sci.USA, 118, 2021

5E9D

RD-1 Mart-1 High bound to Mart-1 decameric peptide (ELA) in complex with HLA-A2
Descriptor:	A6-TCR Valpha, A6-TCR Vbeta, Beta-2-microglobulin, ...
Authors:	Singh, N.K, Baker, B.M.
Deposit date:	2015-10-15
Release date:	2016-06-08
Last modified:	2023-09-27
Method:	X-RAY DIFFRACTION (2.51 Å)
Cite:	An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry. Structure, 24, 2016

5JZI

Crystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 antigen peptide
Descriptor:	Beta-2-microglobulin, HCV1406 TCR alpha chain, HCV1406 TCR beta chain, ...
Authors:	Wang, Y, Piepenbrink, K.H, Baker, B.M.
Deposit date:	2016-05-16
Release date:	2017-05-31
Last modified:	2023-09-27
Method:	X-RAY DIFFRACTION (2.5 Å)
Cite:	How an alloreactive T-cell receptor achieves peptide and MHC specificity. Proc. Natl. Acad. Sci. U.S.A., 114, 2017

7RE8

Class I MHC (HLA-A*02) presenting alpha fetoprotein peptide (AFP)
Descriptor:	Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, MHC class I antigen, ...
Authors:	Dasgupta, M, Baker, B.M.
Deposit date:	2021-07-12
Release date:	2022-07-27
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.82 Å)
Cite:	Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma. Sci Rep, 12, 2022

7RE9

TCR mimic antibody (Fab fragment)
Descriptor:	DI(HYDROXYETHYL)ETHER, Fab heavy chain, Fab light chain
Authors:	Dasgupta, M, Baker, B.M.
Deposit date:	2021-07-12
Release date:	2022-07-27
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.77 Å)
Cite:	Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma. Sci Rep, 12, 2022

7RE7

TCR mimic antibody (Fab fragment) in complex with AFP/HLA-A*02
Descriptor:	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Beta-2-microglobulin, FORMIC ACID, ...
Authors:	Dasgupta, M, Baker, B.M.
Deposit date:	2021-07-12
Release date:	2022-07-27
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.547 Å)
Cite:	Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma. Sci Rep, 12, 2022

7RRG

Crystal structure of human 0606T1-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide
Descriptor:	Beta-2-microglobulin, GLYCEROL, HLA class I histocompatibility antigen, ...
Authors:	Ma, J, Baker, B.M.
Deposit date:	2021-08-09
Release date:	2022-03-23
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.12 Å)
Cite:	Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA. Nat Med, 28, 2022

7RK7

The complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide
Descriptor:	Beta-2-microglobulin, HLA class I histocompatibility antigen, A alpha chain, ...
Authors:	Singh, N.K, Davancaze, L.M, Arbuiso, A, Weiss, L.I, Keller, G.L.J, Baker, B.M.
Deposit date:	2021-07-22
Release date:	2022-11-02
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.54 Å)
Cite:	The complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide To Be Published

6P64

Alpha-beta TCR Binding to Neoantigen KQWLVWLFL Presented by HLA-A206
Descriptor:	302TIL TCR alpha chain, 302TIL TCR beta chain, Beta-2-microglobulin, ...
Authors:	Devlin, J.R, Baker, B.M.
Deposit date:	2019-05-31
Release date:	2020-06-03
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (3.05 Å)
Cite:	A T cell receptor peptide/MHC complex at 3.05 Angstrom resolution To be Published

6PTE

Crystal Structure of ILNAMITKI peptide bound to HLA-A2
Descriptor:	Beta-2-microglobulin, GLYCEROL, HAUS augmin-like complex subunit 3, ...
Authors:	Smith, A.R, Arbuiso, A, Keller, G.L.J, Baker, B.M.
Deposit date:	2019-07-15
Release date:	2019-09-04
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (1.901 Å)
Cite:	Structure Based Prediction of Neoantigen Immunogenicity. Front Immunol, 10, 2019

12 3 4 >

Total results:	86
Displayed results:	25
Sorted by:	Hit score (from highest)
Deposition authors:	"Baker, B.M."