SMTL ID : 6bga.1

2B4 I-Ek TCR-MHC complex with affinity-enhancing Velcro peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

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

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 7 residues within 4Å: Chain A: I.4, E.6 Chain B: N.44, G.45, T.46, Q.47, Y.108 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.47 Hydrogen bonds: B:T.46, B:Q.47, B:Y.108, A:I.4, B:N.44 Water bridges: B:Y.108, B:D.112 NAG-FUC.2: 4 residues within 4Å: Chain C: E.10, S.12, R.27, N.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.27

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81 NAG.4: 2 residues within 4Å: Chain A: N.121, T.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.121, A:T.123

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain A: V.119, V.120, N.121, D.169, H.170, W.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.169 EDO.6: 6 residues within 4Å: Chain A: D.30 Chain B: Y.148, P.149, G.150, R.174, F.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.150, B:R.174 Water bridges: B:Y.148 EDO.7: 5 residues within 4Å: Chain A: R.47, R.97, S.136, Y.153 Chain B: D.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.47, A:R.47, A:R.97

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 6 residues within 4Å: Chain A: E.7, H.8, T.9 Chain B: H.41, F.42, Y.43 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.9, B:F.42 Salt bridges: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gee, M.H. et al., Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-07-18

Peptides

H-2 class II histocompatibility antigen, E-K alpha chain: A
2B4 peptide,MHC I-Ek B chain: B
T cell receptor 2B4 alpha chain: C
T cell receptor 2B4 beta chain: D
Velcro peptide: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

H-2 class II histocompatibility antigen, E-K alpha chain

2B4 peptide,MHC I-Ek B chain

T cell receptor 2B4 alpha chain

T cell receptor 2B4 beta chain

Velcro peptide

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