SMTL ID : 3okt.2 (1 other biounit)

Mouse Plexin A2, extracellular domains 1-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: T.43, G.44, N.45, T.47 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.45 Hydrogen bonds: A:T.47 NAG.2: 4 residues within 4Å: Chain A: K.61, N.80, V.82, N.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.61 NAG.3: 1 residues within 4Å: Chain A: N.296 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.567 No protein-ligand interaction detected (PLIP) NAG.5: 6 residues within 4Å: Chain A: I.593, L.595, N.624, S.626, A.627, Q.629 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.593 Hydrogen bonds: A:N.624, A:Q.629 NAG.13: 4 residues within 4Å: Chain B: T.43, G.44, N.45, T.47 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.45 NAG.14: 4 residues within 4Å: Chain B: K.61, N.80, V.82, N.132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.61 NAG.15: 1 residues within 4Å: Chain B: N.296 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain B: N.567 No protein-ligand interaction detected (PLIP) NAG.17: 6 residues within 4Å: Chain B: I.593, L.595, N.624, S.626, A.627, Q.629 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.593 Hydrogen bonds: B:N.624, B:Q.629

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

CL.6: 3 residues within 4Å: Chain A: Q.314, Y.315, H.316 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.428 Chain B: I.525 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: Q.314, Y.315, H.316 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: I.525 Chain B: R.428 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 1 residues within 4Å: Chain A: N.519 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.519 NA.20: 1 residues within 4Å: Chain B: N.519 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.519

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: I.87, I.88, G.139, V.140, I.141 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.88, A:G.139, A:I.141 GOL.10: 5 residues within 4Å: Chain A: T.23, L.86, I.87, I.88 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.88 Water bridges: A:L.86, A:Y.138 GOL.11: 4 residues within 4Å: Chain A: Q.314, H.317, P.318, D.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.314, A:R.400 Water bridges: A:D.320, A:D.320 GOL.12: 3 residues within 4Å: Chain A: Y.412, R.428, G.493 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.412 GOL.21: 6 residues within 4Å: Chain B: I.87, I.88, G.139, V.140, I.141 Ligands: GOL.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.88, B:G.139, B:I.141 GOL.22: 5 residues within 4Å: Chain B: T.23, L.86, I.87, I.88 Ligands: GOL.21 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.23, B:I.88 Water bridges: B:L.86, B:Y.138 GOL.23: 4 residues within 4Å: Chain B: Q.314, H.317, P.318, D.320 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.314, B:R.400 Water bridges: B:D.320, B:D.320 GOL.24: 3 residues within 4Å: Chain B: Y.412, R.428, G.493 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.412, B:Y.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janssen, B.J. et al., Structural basis of semaphorin-plexin signalling. Nature (2010)

Release Date

2010-10-13

Peptides

Plexin-A2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Plexin-A2

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