SMTL ID : 3qib.1

Crystal structure of the 2B4 TCR in complex with MCC/I-Ek

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

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

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 5 residues within 4Å: Chain A: I.1, K.2 Chain B: N.23, Q.26 Ligands: FUC.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.2 Hydrogen bonds: A:I.1, B:N.23 NAG.4: 4 residues within 4Å: Chain C: E.17, D.114 Ligands: FUC.5, BMA.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.17, C:D.114

2 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.2: 8 residues within 4Å: Chain A: I.1, E.3 Chain B: N.23, G.24, T.25, Q.26, Y.87 Ligands: NAG.1 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.26 Hydrogen bonds: B:T.25, B:Q.26 FUC.5: 5 residues within 4Å: Chain C: D.114, Q.116, D.169, K.171 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.114, C:Q.116, C:K.171

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: T.6 Chain B: E.18, H.20, R.33, R.43 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.6, B:R.33, B:R.43 PEG.7: 7 residues within 4Å: Chain C: T.102, F.103, G.104, Q.105 Chain D: N.67, E.68, F.69 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:F.103, C:Q.105, D:F.69 Water bridges: C:K.100, C:K.100 PEG.8: 7 residues within 4Å: Chain C: R.24, N.26, F.27, T.28, E.69, S.70, Y.71 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.24, C:E.69 PEG.9: 6 residues within 4Å: Chain C: V.147, S.148, Q.149, I.157, D.159 Chain D: L.203 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.147, C:Q.149 PEG.10: 6 residues within 4Å: Chain D: Q.62, N.64, E.68, K.70, S.113, A.114 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.64, D:S.113 PEG.11: 5 residues within 4Å: Chain D: Y.36, D.179, V.181, E.182, P.202 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.36 PEG.12: 5 residues within 4Å: Chain C: G.43 Chain D: Q.63, N.64, K.65, L.115 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.115

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.6: 3 residues within 4Å: Chain C: D.114, Q.116 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.114, C:Q.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newell, E.W. et al., Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k). J.Immunol. (2011)

Release Date

2011-04-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
P

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

MHC class II E-beta-k

T-cell receptor alpha chain C region

2B4 beta chain

MCC peptide

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