SMTL ID : 5c14.1 (2 other biounits)

Crystal structure of PECAM-1 D1D2 domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Y.51, K.83, T.85, E.92, T.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.83, A:E.92 GOL.2: 4 residues within 4Å: Chain A: N.24, V.105, P.106, S.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.24, A:S.107, A:S.107 GOL.3: 5 residues within 4Å: Chain A: K.52, F.57, Y.69, D.78, Y.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.69, A:D.78, A:Y.82

1 x CU: COPPER (II) ION(Non-covalent)

CU.4: 2 residues within 4Å: Chain A: E.73, D.78 No protein-ligand interaction detected (PLIP)

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

NAG.5: 3 residues within 4Å: Chain A: K.26, N.27, F.70 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.26 Hydrogen bonds: A:N.27 NAG.6: 2 residues within 4Å: Chain A: Q.47, N.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.47, A:N.59 NAG.7: 5 residues within 4Å: Chain A: T.111, N.126, S.128, F.163, I.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.111, A:S.128

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 3 residues within 4Å: Chain A: W.20, Y.98, Q.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.20, A:Q.99, A:Q.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paddock, C. et al., Structural basis for PECAM-1 homophilic binding. Blood (2016)

Release Date

2016-01-06

Peptides

Platelet endothelial cell adhesion molecule: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Platelet endothelial cell adhesion molecule

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