SMTL ID : 4z77.2 (1 other biounit)

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-oligomer

Ligands

1 x LEU- TYR- LEU- VAL- CYS- GLY- GLU- ARG- VAL: Insulin(Non-covalent)

LEU-TYR-LEU-VAL-CYS-GLY-GLU-ARG-VAL.1: 28 residues within 4Å: Chain A: L.6, Y.8, V.10, F.23, A.25, F.46, Q.64, R.67, D.71, W.74, V.77, S.78, T.81, Y.85, F.96, R.98, F.100, Y.124, T.144, K.147, W.148, D.153, Y.156, Y.157, Y.160, W.168, Y.172 Ligands: 15P.4 40 PLIP interactions: 40 interactions with chain A Hydrophobic interactions: A:Y.8, A:V.10, A:A.25, A:F.46, A:R.67, A:D.71, A:W.74, A:V.77, A:T.81, A:Y.85, A:F.96, A:F.100, A:F.100, A:Y.156, A:Y.157, A:Y.160, A:Y.160, A:W.168, A:W.168 Hydrogen bonds: A:Y.8, A:Y.8, A:Q.64, A:Q.64, A:D.71, A:D.71, A:D.71, A:S.78, A:R.98, A:R.98, A:D.153, A:Y.156, A:Y.157, A:Y.172 Water bridges: A:W.74, A:W.74, A:T.81, A:K.147, A:K.147, A:Y.157 Salt bridges: A:K.147

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: P.51, W.52, Q.55, E.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.178 GOL.3: 5 residues within 4Å: Chain A: L.110, L.111, E.129, L.131, E.162 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.110 GOL.10: 2 residues within 4Å: Chain B: S.58, D.60 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.7, B:D.60, B:D.60 Water bridges: B:G.30, B:K.59

2 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.4: 2 residues within 4Å: Chain A: A.151 Ligands: LEU-TYR-LEU-VAL-CYS-GLY-GLU-ARG-VAL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.151 15P.5: 3 residues within 4Å: Chain A: E.164, E.167, W.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.164, A:W.168 Water bridges: A:E.164

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

EDO.6: 5 residues within 4Å: Chain A: F.9, Y.28, D.30, D.31 Chain B: K.59 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.31, B:K.59 Water bridges: B:Y.64 EDO.7: 4 residues within 4Å: Chain A: Y.28, P.236 Chain B: S.53, Y.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.28 Water bridges: A:Q.33 EDO.8: 4 residues within 4Å: Chain A: S.93, T.95, D.120 Chain B: P.33 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.95, A:T.95, A:D.120 Water bridges: B:I.2 EDO.11: 7 residues within 4Å: Chain A: V.232, R.235, W.245 Chain B: Q.9, V.10, V.94, M.100 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.235, A:W.245, B:V.10 EDO.12: 7 residues within 4Å: Chain B: L.41, K.42, N.43, G.44, E.78, Y.79, A.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.41, B:G.44

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 3 residues within 4Å: Chain A: R.84, Y.85, N.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.87 SO4.13: 4 residues within 4Å: Chain A: D.123 Chain B: K.59, D.60, W.61 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.116, B:K.59 SO4.14: 4 residues within 4Å: Chain B: E.37, D.39, R.46, R.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.82 Water bridges: B:V.38 Salt bridges: B:R.46 SO4.15: 6 residues within 4Å: Chain B: F.23, K.49, E.51, Y.68, T.69, E.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.51, B:E.51, B:T.69, B:E.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizkallah, P.J. et al., Weak TCR binding to an unstable insulin epitope drives type 1 diabetes. To Be Published

Release Date

2015-06-24

Peptides

H-2 class I histocompatibility antigen, K-D alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

H-2 class I histocompatibility antigen, K-D alpha chain

Beta-2-microglobulin

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