SMTL ID : 6qp8.1

Drosophila Semaphorin 2b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 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: 4 residues within 4Å: Chain A: Q.34, N.70, S.72, Q.73 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.137, N.139, T.141 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: Q.34, N.70, S.72, Q.73 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.137, N.139, T.141 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

NAG-NAG-BMA-MAN-MAN.3: 9 residues within 4Å: Chain A: A.164, N.166, F.191, N.230, R.246, Q.305, T.325, I.415, T.441 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.415, A:T.441

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.4: 20 residues within 4Å: Chain A: R.288, N.290, S.292, S.294, S.295, E.296, P.298, Y.300, K.350, W.359, L.360, P.361, D.397, A.399, H.402 Chain B: D.227, H.248, I.253, N.254, K.257 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.300 Hydrogen bonds: B:K.257, A:E.296

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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

NAG-NAG-BMA-MAN-MAN-MAN.5: 5 residues within 4Å: Chain A: F.178, G.179, N.205, T.207, N.208 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.207

2 x NAG- NAG- BMA- MAN: 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

NAG-NAG-BMA-MAN.6: 5 residues within 4Å: Chain A: N.540, K.578, Q.579, D.627, T.629 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.627 Hydrogen bonds: A:Q.579, A:R.581, A:R.581, A:Q.579 NAG-NAG-BMA-MAN.9: 8 residues within 4Å: Chain B: A.164, N.166, N.230, R.246, Q.305, I.415, T.441, H.470 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.415, B:T.441 Hydrogen bonds: B:H.470

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

NAG-NAG-MAN-MAN-MAN-MAN-MAN-MAN.10: 20 residues within 4Å: Chain A: D.227, H.248, I.253, N.254, K.257 Chain B: R.288, N.290, S.292, S.294, S.295, E.296, P.298, Y.300, K.350, W.359, L.360, P.361, D.397, A.399, H.402 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.295, B:E.296

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.11: 5 residues within 4Å: Chain B: F.178, G.179, N.205, T.207, N.208 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.207

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.12: 6 residues within 4Å: Chain B: N.540, K.578, R.581, D.627, G.628, T.629 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.581, B:D.627

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

NAG.13: 1 residues within 4Å: Chain A: N.377 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.377 NAG.15: 1 residues within 4Å: Chain B: N.377 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.377 Water bridges: B:N.269, B:N.377

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 9 residues within 4Å: Chain A: Y.47, D.49, Y.56, P.113, M.114, Q.119, K.120, L.121, A.138 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.49, A:D.49, A:Y.56, A:Y.56, A:M.114, A:K.120 GOL.16: 8 residues within 4Å: Chain B: Y.122, D.133, I.152, K.158, Y.171, L.183, S.201, L.206 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.122, B:D.133, B:K.158, B:Y.171, B:L.183, B:S.201 Water bridges: B:Y.204 GOL.17: 7 residues within 4Å: Chain B: K.316, Y.318, E.403, F.404, L.434, Q.450, M.452 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.403, B:Q.450 Water bridges: B:S.335, B:E.432, B:R.457

1 x FLC: CITRATE ANION(Non-covalent)

FLC.18: 4 residues within 4Å: Chain B: K.316, R.339, K.423, E.432 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.316 Water bridges: B:K.423, B:E.432 Salt bridges: B:K.316, B:K.316, B:R.339, B:K.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rozbesky, D. et al., Diversity of oligomerization in Drosophila semaphorins suggests a mechanism of functional fine-tuning. Nat Commun (2019)

Release Date

2019-08-21

Peptides

IP13724p: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

IP13724p