SMTL ID : 4gz8.1

Mouse Semaphorin 3A, domains Sema-PSI-IG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

1 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: 5 residues within 4Å: Chain A: N.36, H.59, K.73, V.75, P.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.73

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: Y.107, N.108, T.110, H.111, Y.126, Q.141 No protein-ligand interaction detected (PLIP)

1 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(Non-covalent)

NAG-NAG-BMA-MAN.3: 5 residues within 4Å: Chain B: N.36, H.59, K.73, V.75, P.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.73

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: D.293, Q.416 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.293, A:D.293 CA.5: 1 residues within 4Å: Chain A: E.105 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.105, A:E.105 CA.6: 5 residues within 4Å: Chain A: N.32, L.34, S.37, Y.40, T.489 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.37 CA.8: 2 residues within 4Å: Chain B: D.293, Q.416 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.293, B:D.293 CA.9: 1 residues within 4Å: Chain B: E.105 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.105, B:E.105

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 8 residues within 4Å: Chain A: N.27, K.443, E.461, M.463, P.496, L.497, H.498, R.499 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27, A:P.496, A:R.499 Salt bridges: A:K.443 ACT.11: 6 residues within 4Å: Chain B: N.27, K.443, E.461, M.463, P.496, L.497 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.27, B:E.461

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

NAG.10: 5 residues within 4Å: Chain B: Y.107, N.108, T.110, H.111, Y.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.110, B:Y.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janssen, B.J.C. et al., Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-10-17

Peptides

Semaphorin-3A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Semaphorin-3A