SMTL ID : 5c14.3 (2 other biounits)

Crystal structure of PECAM-1 D1D2 domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Y.51, K.83, T.85, E.92, T.94 Chain C: R.124, E.167 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.83, A:E.92, C:E.167 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 GOL.9: 3 residues within 4Å: Chain B: R.75, E.131 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.75, B:R.75, B:E.131 Water bridges: B:E.73 GOL.10: 4 residues within 4Å: Chain B: Q.23, N.24, G.104 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.24 GOL.13: 7 residues within 4Å: Chain A: R.124, E.167 Chain C: Y.51, K.83, T.85, E.92, T.94 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.51, C:K.83, C:T.85, C:E.92, A:E.167 GOL.14: 4 residues within 4Å: Chain C: N.24, V.105, P.106, S.107 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.24, C:S.107, C:S.107 GOL.15: 5 residues within 4Å: Chain C: K.52, F.57, Y.69, D.78, Y.82 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.82, C:Y.82 GOL.21: 3 residues within 4Å: Chain D: R.75, E.131 Ligands: GOL.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.73, D:R.75, D:R.75 Water bridges: D:E.73 GOL.22: 4 residues within 4Å: Chain D: Q.23, N.24, G.104 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.24

2 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) CU.16: 2 residues within 4Å: Chain C: E.73, D.78 No protein-ligand interaction detected (PLIP)

10 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: 6 residues within 4Å: Chain A: T.111, N.126, S.128, F.163, I.165 Chain C: V.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.111, A:S.128 NAG.11: 2 residues within 4Å: Chain B: N.27, F.70 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.70 NAG.12: 1 residues within 4Å: Chain B: N.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.59 NAG.17: 3 residues within 4Å: Chain C: K.26, N.27, F.70 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.26 Hydrogen bonds: C:N.27 NAG.18: 2 residues within 4Å: Chain C: Q.47, N.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.47, C:N.59 NAG.19: 6 residues within 4Å: Chain A: V.55 Chain C: T.111, N.126, S.128, F.163, I.165 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.111, C:S.128 NAG.23: 2 residues within 4Å: Chain D: N.27, F.70 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.70 NAG.24: 1 residues within 4Å: Chain D: N.59 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.59

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Platelet endothelial cell adhesion molecule

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