SMTL ID : 3okw.1

Mouse Semaphorin 6A, extracellular domains 1-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 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: 7 residues within 4Å: Chain A: R.265, N.267, S.269, H.275, Y.277, A.386, N.392 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: Y.417, N.419, E.543 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.417 NAG-NAG.3: 2 residues within 4Å: Chain B: N.50, K.111 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain B: R.265, N.267, S.269, H.275, Y.277, A.386, N.392 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN.5: 4 residues within 4Å: Chain B: R.438, G.440, S.441, N.446 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: N.50, R.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.50 NAG.14: 4 residues within 4Å: Chain B: Y.417, N.419, H.420, E.543 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.543, B:E.543

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.7: 5 residues within 4Å: Chain A: H.39, R.40, K.99, D.100, H.103 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.39, A:R.40, A:R.40 Salt bridges: A:H.39, A:R.40, A:R.40, A:K.99, A:H.103

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: R.58, D.59, H.60, K.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.59, A:K.83, A:K.83 GOL.9: 8 residues within 4Å: Chain A: M.45, K.107, V.108, L.109, L.110, N.158, I.159, A.160 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.109, A:L.109, A:N.158, A:N.158, A:A.160 Water bridges: A:A.160 GOL.10: 4 residues within 4Å: Chain A: A.87, D.88, T.91, N.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.88, A:T.91, A:T.91, A:N.126 Water bridges: A:D.88 GOL.11: 2 residues within 4Å: Chain A: Y.213, G.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.214 GOL.12: 3 residues within 4Å: Chain A: S.274, H.275, Y.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.275, A:H.275, A:Y.277 GOL.13: 5 residues within 4Å: Chain A: D.42, Q.44, D.100, E.101, F.105 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.44, A:D.100 Water bridges: A:D.153, A:A.154, A:S.489 GOL.15: 3 residues within 4Å: Chain B: D.174, F.175, L.176 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.174, B:L.176 Water bridges: B:F.175, B:F.175 GOL.16: 5 residues within 4Å: Chain B: Q.44, D.100, E.101, F.105, A.154 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.44, B:D.100 Water bridges: B:D.153, B:A.154 GOL.17: 8 residues within 4Å: Chain B: M.45, K.107, V.108, L.109, L.110, N.158, I.159, A.160 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.107, B:L.109, B:L.109, B:A.160 Water bridges: B:N.158 GOL.18: 3 residues within 4Å: Chain B: D.88, T.91, N.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.126 Water bridges: B:D.88, B:T.91

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

Semaphorin-6A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Semaphorin-6A

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