SMTL ID : 4nqd.5 (4 other biounits)

Crystal structure of TCR-MR1 ternary complex and non-covalently bound 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-oligomer

Ligands

2 x 2LJ: 1-DEOXY-1-({2,6-DIOXO-5-[(E)-(2-OXOPROPYLIDENE)AMINO]-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL}AMINO)-D-RIBITOL(Non-covalent)

2LJ.1: 14 residues within 4Å: Chain A: Y.8, R.10, S.25, T.35, H.59, Y.63, L.67, W.70, R.95, I.97, Y.153, Q.154, W.157 Chain B: Y.95 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.63 Hydrogen bonds: A:R.10, A:S.25, A:S.25, A:T.35, A:R.95, A:R.95, A:Y.153, A:Q.154, A:Q.154, A:W.157 Water bridges: A:Y.8, A:R.10, A:Y.63, A:W.70 pi-Stacking: A:Y.8 2LJ.3: 16 residues within 4Å: Chain E: Y.8, R.10, S.25, T.35, H.59, W.60, Y.63, L.67, W.70, R.95, I.97, Y.153, Q.154, W.157 Chain G: Y.95 Chain H: G.98 17 PLIP interactions: 15 interactions with chain E, 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: E:Y.63 Hydrogen bonds: E:R.10, E:S.25, E:S.25, E:T.35, E:R.95, E:R.95, E:Y.153, E:Q.154, E:W.157, H:G.98, G:Y.95 Water bridges: E:R.10, E:G.27, E:Y.63, E:Y.63 pi-Stacking: E:Y.8

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain B: Y.24, Q.25, T.26, G.28, F.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.26, B:T.26, B:G.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Corbett, A.J. et al., T-cell activation by transitory neo-antigens derived from distinct microbial pathways. Nature (2014)

Release Date

2014-04-16

Peptides

Major histocompatibility complex class I-related gene protein: AE
TCR alpha chain: BG
TCR beta chain: CH
Beta-2-microglobulin: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

E
A

B
D

G
G

C
E

H
H

D
F

F
B

Major histocompatibility complex class I-related gene protein

TCR alpha chain

TCR beta chain

Beta-2-microglobulin

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