SMTL ID : 5c0i.1

HAL-A02 carrying RQFGPDFPTI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: E.213, I.214, T.215, Q.263, H.264, E.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.215 Water bridges: A:E.265 EDO.2: 3 residues within 4Å: Chain A: S.106, D.107, W.108 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: M.139, Q.142, T.143, H.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.139, A:T.143, A:T.143 EDO.4: 4 residues within 4Å: Chain A: R.15, R.18, G.19, E.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:E.20 EDO.5: 6 residues within 4Å: Chain A: R.45, M.46, E.47, P.48, W.61, T.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.45, A:R.45 EDO.11: 9 residues within 4Å: Chain A: W.205, L.207, R.235, Q.243 Chain B: Y.11, S.12, H.14, P.15, M.100 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.12, B:H.14, A:R.235, A:Q.243 Water bridges: B:M.100 EDO.12: 5 residues within 4Å: Chain A: R.22, I.24 Chain B: S.34, D.35 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.34, B:D.35 Water bridges: B:S.34, B:I.36 EDO.13: 4 residues within 4Å: Chain B: T.74, W.96, D.97, R.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.74, B:R.98, B:R.98 EDO.14: 5 residues within 4Å: Chain A: Q.116 Chain B: F.57, S.58, K.59, W.61 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.61 EDO.15: 4 residues within 4Å: Chain A: Y.28, P.236 Chain B: S.53, Y.64 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.28, B:S.53 Hydrogen bonds: B:S.53

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: R.7, F.9, Y.28, D.30, D.31 Chain B: Y.64 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.7, A:D.30, B:Y.64, B:Y.64 GOL.7: 4 residues within 4Å: Chain A: K.69, A.70, S.72, Q.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.72, A:Q.73 Water bridges: A:K.69, A:A.70, A:A.70 GOL.16: 7 residues within 4Å: Chain B: Q.9, V.10, V.94, K.95, W.96, D.97, M.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.10, B:D.97 GOL.17: 9 residues within 4Å: Chain A: R.22, I.24, D.38 Chain B: H.52, S.53, D.54, L.55, L.65 Ligands: EDO.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.52, B:D.54, B:L.55, A:D.38

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

SO4.8: 3 residues within 4Å: Chain A: E.167, W.168, R.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.168 Salt bridges: A:R.171 SO4.9: 5 residues within 4Å: Chain A: E.129, D.130, L.131, R.132, E.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.130 Salt bridges: A:R.132

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 3 residues within 4Å: Chain B: N.84, H.85, L.88 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.85, B:L.88, H2O.10, H2O.10, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cole, D.K. et al., Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. J.Clin.Invest. (2016)

Release Date

2016-05-04

Peptides

HLA class I histocompatibility antigen, A-2 alpha chain: A
Beta-2-microglobulin: B
Marker peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

Marker peptide

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