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SMTL ID : 9o5s.2 (3 other biounits)

minibinder-antigen complex BXMart1-3-MART1-HLA*A02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1:	3 residues within 4Å: Chain A: T.183, D.184, A.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.185
GOL.2:	6 residues within 4Å: Chain A: R.7, F.9, Y.28, D.30, D.31 Chain B: Y.63 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.63, A:D.31 Water bridges: A:D.30
GOL.3:	4 residues within 4Å: Chain A: G.238 Chain B: S.52, L.65, Y.67 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.49, B:Y.67 Water bridges: A:G.240
GOL.4:	5 residues within 4Å: Chain A: R.22 Chain B: S.33, I.35, H.51, L.64 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.33, B:I.35, B:H.51, B:L.54 Water bridges: A:D.38
GOL.5:	4 residues within 4Å: Chain B: E.36, N.83 Chain D: Q.44, D.46 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:D.34, B:N.83, D:Q.44 Water bridges: B:V.85, D:L.47
GOL.6:	6 residues within 4Å: Chain D: R.38, Q.39, T.40, K.43, Q.44, D.46 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.38, D:R.38, D:T.40, D:D.46

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Liu, B. et al., Design of high specificity binders for peptide-MHC-I complexes. Science (2025)

Release Date

2025-07-23

Peptides

HLA class I histocompatibility antigen, A alpha chain: A
Beta-2-microglobulin: B
Melanoma antigen recognized by T-cells 1: C
antibody AD01: D
BXMart1-3 minibinder: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
T

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

HLA class I histocompatibility antigen, A alpha chain

Beta-2-microglobulin

Melanoma antigen recognized by T-cells 1

antibody AD01

BXMart1-3 minibinder

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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