SMTL ID : 6qp7.1

Drosophila Semaphorin 2a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 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: 3 residues within 4Å: Chain A: N.72, S.74, S.75 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: Y.138, N.140, T.142 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.72, S.74, S.75 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: N.540, S.543, E.578, G.627, G.628 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.625

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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.3: 9 residues within 4Å: Chain A: L.165, D.166, N.167, K.194, N.231, R.247, Q.306, N.327, N.442 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.442 NAG-NAG-BMA-MAN-MAN-MAN.4: 16 residues within 4Å: Chain A: R.289, N.291, S.293, S.295, G.296, E.297, F.298, P.299, Y.301, A.400, H.403, N.406 Chain B: K.229, K.258 Ligands: EDO.25, EDO.26 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.296, B:K.258, A:E.297 Water bridges: B:K.258

1 x NAG- NAG- BMA- 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)]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.6: 3 residues within 4Å: Chain B: Y.138, N.140, T.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.138

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.7: 9 residues within 4Å: Chain B: L.165, D.166, N.167, K.194, N.231, R.247, Q.306, N.442 Ligands: EDO.28 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.442

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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.8: 19 residues within 4Å: Chain A: D.228, K.229, T.249, I.254, N.255, G.257, K.258 Chain B: R.289, N.291, S.293, S.295, G.296, E.297, P.299, Y.301, A.400, N.402, H.403, N.406 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:K.258, B:Y.301 Hydrogen bonds: B:G.296, A:K.258, A:K.258

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

NAG.10: 4 residues within 4Å: Chain A: K.461, N.540, E.578, G.627 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.461, A:N.540, A:G.627 NAG.24: 4 residues within 4Å: Chain B: L.181, N.206, A.209, R.211 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.181 Hydrogen bonds: B:N.206, B:N.206, B:R.211, B:R.211

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 7 residues within 4Å: Chain A: K.229, N.231, R.247, E.248, T.249, V.260 Ligands: EDO.13 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: L.85, E.86, T.88, N.128, K.133, Y.135 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: V.260, E.304 Chain B: F.298 Ligands: EDO.11 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: Y.11, N.508, C.509, F.510, W.520, C.546, S.549, L.631 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: Y.135, V.136, I.137, Y.143, L.144, Y.149 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: V.580, T.581, W.582, E.593, I.594, R.595, Y.596 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: P.299, F.300, Y.301 Chain B: T.326 Ligand excluded by PLIP EDO.18: 10 residues within 4Å: Chain A: R.111, V.112, K.159, C.160, P.161, S.168, T.169, A.170, G.187, T.188 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: Y.253, Y.261, R.289, Y.301, N.303 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: Y.410, Y.411 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: V.251, I.254, N.255, Q.353, S.356, W.360 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: F.298 Chain B: R.247, V.260, E.304 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4, EDO.26 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain B: K.229, N.231, R.247, E.248, T.249, V.260 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4, EDO.25 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain B: P.161, D.166, N.167, S.168, T.188, N.189, P.230, F.232 Ligands: EDO.28 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: D.166, K.194, K.229, P.230, N.231 Ligands: NAG-NAG-BMA.7, EDO.27 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain B: V.580, T.581, W.582, E.593, I.594, R.595, Y.596 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain B: Y.301, F.302, N.303, T.323, T.324, S.325, T.326 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: Y.135, V.136, Y.143, L.144, Y.149 Ligand excluded by PLIP

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

CL.22: 6 residues within 4Å: Chain A: L.43, Y.44, A.61, M.62, H.109, R.111 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: K.349, N.365 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain B: R.505, N.508, R.511, F.568 Ligand excluded by PLIP CL.33: 5 residues within 4Å: Chain B: Y.44, A.61, M.62, H.109, R.111 Ligand excluded by PLIP

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

Semaphorin-2A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Semaphorin-2A