SMTL ID : 5l5c.1

Plexin A1 full extracellular region, domains 1 to 10, to 6 angstrom, spacegroup P4(3)2(1)2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 6.00 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG- BMA- MAN: 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.1: 3 residues within 4Å: Chain A: R.7, N.42, T.44 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.3: 5 residues within 4Å: Chain A: N.562, E.570, T.571, E.572, K.610 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 3 residues within 4Å: Chain B: R.7, N.42, T.44 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 5 residues within 4Å: Chain B: N.562, E.570, T.571, E.572, K.610 No protein-ligand interaction detected (PLIP)

4 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.2: 5 residues within 4Å: Chain A: Q.534, P.535, R.536, N.537, S.639 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 4 residues within 4Å: Chain A: F.725, N.726, S.729, Q.731 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.12: 5 residues within 4Å: Chain B: Q.534, P.535, R.536, N.537, S.639 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 4 residues within 4Å: Chain B: F.725, N.726, S.729, Q.731 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- MAN- MAN: 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.4: 6 residues within 4Å: Chain A: V.540, A.591, Q.595, N.625, V.628, Q.630 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.8: 6 residues within 4Å: Chain A: R.1017, D.1019, Y.1062, N.1063, T.1065, T.1066 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.14: 6 residues within 4Å: Chain B: V.540, A.591, Q.595, N.625, V.628, Q.630 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.18: 6 residues within 4Å: Chain B: R.1017, D.1019, Y.1062, N.1063, T.1065, T.1066 No protein-ligand interaction detected (PLIP)

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.5: 1 residues within 4Å: Chain A: N.637 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain B: N.637 No protein-ligand interaction detected (PLIP)

2 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: 2 residues within 4Å: Chain A: N.750, N.766 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 2 residues within 4Å: Chain B: N.750, N.766 No protein-ligand interaction detected (PLIP)

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

NAG.9: 2 residues within 4Å: Chain A: V.687, N.734 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: R.935, S.988, N.1008, T.1010 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.935, A:N.1037 NAG.19: 2 residues within 4Å: Chain B: V.687, N.734 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain B: R.935, S.988, N.1008, T.1010 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.935, B:N.1037

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kong, Y. et al., Structural Basis for Plexin Activation and Regulation. Neuron (2016)

Release Date

2016-07-06

Peptides

Plexin-A1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Plexin-A1

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