SMTL ID : 3oky.1

Plexin A2 in complex with Semaphorin 6A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain B: R.265, N.267, S.269, P.271, H.275, Y.277, A.386, N.392 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.271 NAG-NAG.13: 8 residues within 4Å: Chain D: R.265, N.267, S.269, P.271, H.275, Y.277, A.386, N.392 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.271

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

NAG.2: 2 residues within 4Å: Chain A: N.45, T.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.47 Water bridges: A:N.45 NAG.3: 3 residues within 4Å: Chain A: K.61, N.132, K.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.61, A:K.61, A:N.132 Water bridges: A:S.100 NAG.4: 1 residues within 4Å: Chain A: N.296 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.567 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain B: N.50, K.111, D.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.111, B:D.114 NAG.10: 3 residues within 4Å: Chain B: Y.417, N.419, H.420 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.419 NAG.14: 2 residues within 4Å: Chain C: N.45, T.47 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.45 NAG.15: 3 residues within 4Å: Chain C: K.61, N.132, K.133 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.61, C:K.61, C:N.132 Water bridges: C:S.100 NAG.16: 1 residues within 4Å: Chain C: N.296 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain C: N.567 No protein-ligand interaction detected (PLIP) NAG.21: 3 residues within 4Å: Chain D: N.50, K.111, D.114 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.111 NAG.22: 3 residues within 4Å: Chain D: Y.417, N.419, H.420 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.419

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 12 residues within 4Å: Chain A: H.260, S.261, Y.262, V.263, L.340, Y.344, F.373, G.375, I.378, N.379, Q.380, L.382 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.262, A:N.379 GOL.7: 5 residues within 4Å: Chain A: Y.412, L.490, G.493, D.494, P.495 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.412, A:L.490, A:G.493 GOL.8: 7 residues within 4Å: Chain A: R.26, I.88, D.89, Y.90, S.91, I.141, R.143 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.26, A:D.89, A:S.91, A:S.91, A:I.141, A:R.143 Water bridges: A:I.141 GOL.11: 7 residues within 4Å: Chain B: M.45, K.107, V.108, L.109, N.158, I.159, A.160 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.107, B:L.109, B:N.158, B:A.160 Water bridges: B:A.160 GOL.12: 4 residues within 4Å: Chain B: T.285, D.286, A.409, V.410 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.286, B:V.410, B:V.410 Water bridges: B:V.284 GOL.18: 12 residues within 4Å: Chain C: H.260, S.261, Y.262, V.263, L.340, Y.344, F.373, G.375, I.378, N.379, Q.380, L.382 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.262, C:N.379 GOL.19: 5 residues within 4Å: Chain C: Y.412, L.490, G.493, D.494, P.495 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.490, C:G.493 GOL.20: 7 residues within 4Å: Chain C: R.26, I.88, D.89, Y.90, S.91, I.141, R.143 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.26, C:S.91, C:S.91, C:I.141, C:R.143 Water bridges: C:I.141 GOL.23: 7 residues within 4Å: Chain D: M.45, K.107, V.108, L.109, N.158, I.159, A.160 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.107, D:L.109, D:N.158, D:A.160 Water bridges: D:A.160 GOL.24: 4 residues within 4Å: Chain D: T.285, D.286, A.409, V.410 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.286, D:V.410, D:V.410 Water bridges: D:V.284

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: AC
Putative uncharacterized protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Plexin-A2

Putative uncharacterized protein

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