- 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)
- 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
- 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
- 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 PLIPEDO.12: 6 residues within 4Å:- Chain A: L.85, E.86, T.88, N.128, K.133, Y.135
Ligand excluded by PLIPEDO.13: 4 residues within 4Å:- Chain A: V.260, E.304
- Chain B: F.298
- Ligands: EDO.11
Ligand excluded by PLIPEDO.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 PLIPEDO.15: 6 residues within 4Å:- Chain A: Y.135, V.136, I.137, Y.143, L.144, Y.149
Ligand excluded by PLIPEDO.16: 7 residues within 4Å:- Chain A: V.580, T.581, W.582, E.593, I.594, R.595, Y.596
Ligand excluded by PLIPEDO.17: 4 residues within 4Å:- Chain A: P.299, F.300, Y.301
- Chain B: T.326
Ligand excluded by PLIPEDO.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 PLIPEDO.19: 5 residues within 4Å:- Chain A: Y.253, Y.261, R.289, Y.301, N.303
Ligand excluded by PLIPEDO.20: 2 residues within 4Å:- Chain A: Y.410, Y.411
Ligand excluded by PLIPEDO.21: 6 residues within 4Å:- Chain A: V.251, I.254, N.255, Q.353, S.356, W.360
Ligand excluded by PLIPEDO.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 PLIPEDO.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 PLIPEDO.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 PLIPEDO.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 PLIPEDO.29: 7 residues within 4Å:- Chain B: V.580, T.581, W.582, E.593, I.594, R.595, Y.596
Ligand excluded by PLIPEDO.30: 7 residues within 4Å:- Chain B: Y.301, F.302, N.303, T.323, T.324, S.325, T.326
Ligand excluded by PLIPEDO.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 PLIPCL.23: 2 residues within 4Å:- Chain A: K.349, N.365
Ligand excluded by PLIPCL.32: 4 residues within 4Å:- Chain B: R.505, N.508, R.511, F.568
Ligand excluded by PLIPCL.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
AB
B
- 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)
- 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
- 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
- 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
- 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
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 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
AB
B