SMTL ID : 6ddr.1

Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: Q.160, S.162, S.176, S.177, T.178 Chain B: F.170, P.171, V.173, S.181, L.182, S.183 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.160, A:T.178, B:F.170, B:S.181, B:S.183 GOL.2: 5 residues within 4Å: Chain A: Q.37, Q.45, L.47, P.59, F.62 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.37, A:Q.45, A:L.46, A:R.61 GOL.3: 2 residues within 4Å: Chain A: K.190, R.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.211, A:R.211 Water bridges: A:K.190 GOL.4: 6 residues within 4Å: Chain B: T.30, N.52, G.54, S.55 Chain C: R.37, S.42 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.42, B:N.52, B:G.54 Water bridges: C:R.37, C:R.37, C:S.42 GOL.5: 8 residues within 4Å: Chain A: Y.86, F.87, G.99, G.100, G.101 Chain B: Q.39, G.44, L.45 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.99, B:Q.39, B:L.45 Water bridges: A:S.85, A:S.85 GOL.7: 4 residues within 4Å: Chain C: R.30, N.31, I.32, V.53 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.31, C:I.32, C:I.32 GOL.8: 6 residues within 4Å: Chain C: D.46, T.47, Q.48, Q.49, A.66, T.67 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.46, C:A.66 GOL.9: 4 residues within 4Å: Chain C: T.21, R.23, W.64, A.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.21, C:R.23

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

SO4.6: 4 residues within 4Å: Chain B: S.131, L.193, P.217, D.221 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 2 residues within 4Å: Chain C: H.45, D.46 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.45, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lombana, T.N. et al., High-resolution glycosylation site-engineering method identifies MICA epitope critical for shedding inhibition activity of anti-MICA antibodies. MAbs (2019)

Release Date

2018-10-24

Peptides

Anti-MICA Fab fragment light chain clone 13A9: A
Anti-MICA Fab fragment heavy chain clone 13A9: B
MHC class I polypeptide-related sequence A: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Anti-MICA Fab fragment light chain clone 13A9

Anti-MICA Fab fragment heavy chain clone 13A9

MHC class I polypeptide-related sequence A

Related Entries With Identical Sequence