SMTL ID : 6lyn.1 (1 other biounit)

CD146 D4-D5/AA98 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: R.50, Y.59 Chain B: L.98 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.50

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Y.27, I.28, F.29, S.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.29, A:S.77 Water bridges: A:T.30 GOL.8: 8 residues within 4Å: Chain B: N.57 Chain C: V.11, R.12, V.13, A.16, Q.86, L.87 Ligands: EPE.5 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:V.11, C:V.13, B:N.57 GOL.9: 7 residues within 4Å: Chain C: R.64, I.92, F.93, G.94, S.120, G.121, Q.143 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.64, C:I.92, C:S.120, C:Q.143

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.40, Q.43 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: I.28, Y.32 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 11 residues within 4Å: Chain B: S.32, G.33, Y.34, S.35, L.54, S.56, N.57 Chain C: Q.86, L.87, P.142 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33, B:S.35

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

NAG.6: 3 residues within 4Å: Chain C: S.75, G.81, N.83 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.75, C:N.83 NAG.7: 5 residues within 4Å: Chain C: P.96, W.97, M.98, K.101, N.173 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.64, C:W.97, C:M.98, C:N.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structure basis for AA98 inhibition on the activation of endothelial cells mediated by CD146. Iscience (2021)

Release Date

2021-02-24

Peptides

AA98 Fab heavy chain: A
AA98 Fab light chain: B
Cell surface glycoprotein MUC18: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

AA98 Fab heavy chain

AA98 Fab light chain

Cell surface glycoprotein MUC18

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