SMTL ID : 1lk2.1

1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY- ASN- TYR- SER- PHE- TYR- ALA- LEU: INSULIN RECEPTOR, BETA-SUBUNIT(Non-covalent)

GLY-ASN-TYR-SER-PHE-TYR-ALA-LEU.1: 25 residues within 4Å: Chain A: Y.7, V.9, E.24, E.63, K.66, N.70, S.73, F.74, D.77, T.80, L.81, Y.84, V.97, Q.114, Y.116, Y.123, T.143, K.146, W.147, E.152, R.155, L.156, Y.159, W.167, Y.171 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.74, A:F.74, A:D.77, A:L.81, A:V.97, A:Y.116, A:Y.123, A:T.143, A:L.156, A:Y.159, A:Y.159, A:Y.159 Hydrogen bonds: A:Y.7, A:E.24, A:E.63, A:K.66, A:N.70, A:N.70, A:S.73, A:D.77, A:E.152, A:R.155, A:R.155, A:Y.171, A:Y.171 Water bridges: A:D.77, A:T.80, A:Y.116, A:Y.116, A:Y.159, A:Y.159 Salt bridges: A:K.146

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

NAG-FUC.2: 5 residues within 4Å: Chain A: Q.54, K.173, N.174, N.176, A.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.54, A:Q.54, A:K.173, A:K.173, A:N.174, A:N.176

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

NAG.3: 1 residues within 4Å: Chain A: N.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.86

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

PO4.4: 6 residues within 4Å: Chain A: V.12, R.14, R.21, D.39 Chain B: H.34 Ligands: MRD.6 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.39 Water bridges: A:R.21, B:H.34, B:H.34 Salt bridges: A:R.14, A:R.21, B:H.34

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 4 residues within 4Å: Chain A: P.47, R.48, A.49, R.50 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.47 MPD.7: 11 residues within 4Å: Chain A: H.188, W.204, L.206, Q.242 Chain B: Y.10, S.11, H.13, P.14, P.15, W.95, R.97 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.15, B:W.95, B:R.97, A:W.204, A:L.206 Hydrogen bonds: B:S.11, A:Q.242, A:Q.242

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 10 residues within 4Å: Chain A: T.10, V.12, R.21, M.23 Chain B: F.30, P.33, I.35, M.54, I.64 Ligands: PO4.4 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.10, A:V.12, B:F.30, B:I.64 Hydrogen bonds: A:R.21, B:P.33 Water bridges: B:H.34, B:I.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.G. et al., A peptide that antagonizes TCR-mediated reactions with both syngeneic and allogeneic agonists: functional and structural aspects. J.Immunol. (2004)

Release Date

2003-11-11

Peptides

H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN

Beta-2-microglobulin

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