SMTL ID : 3nvn.1

Molecular mechanism of guidance cue recognition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

hetero-1-1-mer

Ligands

3 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Post Translational Modification)

NDG.1: 3 residues within 4Å: Chain A: T.36, E.41, N.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.41, A:N.43 NDG.4: 4 residues within 4Å: Chain B: L.42, N.107, S.109, R.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.42, B:S.109 NDG.9: 2 residues within 4Å: Chain B: R.298, N.373 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.298

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain B: E.267, D.270 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.267, B:D.270, H2O.16, H2O.16

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

NAG.3: 3 residues within 4Å: Chain B: Q.49, N.52, T.54 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.54 NAG.5: 3 residues within 4Å: Chain B: S.112, N.115, S.180 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.180 NAG.6: 4 residues within 4Å: Chain B: W.206, N.207, S.300, Q.303 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.206 Hydrogen bonds: B:N.207, B:Q.303 Water bridges: B:R.232 NAG.7: 4 residues within 4Å: Chain B: N.218, T.220, S.221, T.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.218, B:S.221 NAG.8: 1 residues within 4Å: Chain B: N.352 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Structural Basis of Semaphorin-Plexin Recognition and Viral Mimicry from Sema7A and A39R Complexes with PlexinC1. Cell(Cambridge,Mass.) (2010)

Release Date

2010-09-15

Peptides

EVM139: A
Plexin-C1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

EVM139

Plexin-C1

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