SMTL ID : 8ckl.1

Semaphorin-5A TSR 3-4 domains in complex with sucrose octasulfate (SOS)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-dimer

Ligands

1 x YYJ- GU4: 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose-(1-2)-1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose(Non-covalent)

YYJ-GU4.1: 7 residues within 4Å: Chain A: E.55, K.57, T.84, K.86 Chain B: G.98, R.99, R.101 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.57, A:K.57, A:K.86, A:K.86, B:R.99, B:R.101, B:R.101, A:K.86, A:K.86 Hydrogen bonds: B:R.99

4 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.2: 3 residues within 4Å: Chain A: T.9, G.10, W.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.9, A:W.11 MAN.3: 4 residues within 4Å: Chain A: F.7, W.8, R.30, A.39 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.8, A:W.8, A:R.30, A:R.30 MAN.4: 3 residues within 4Å: Chain B: W.8, R.30, A.39 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.8, B:W.8, B:R.30, B:R.30 MAN.5: 3 residues within 4Å: Chain B: G.10, W.11, R.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.11, B:W.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagy, G.N. et al., Structure and function of Semaphorin-5A glycosaminoglycan interactions. Nat Commun (2024)

Release Date

2024-02-28

Peptides

Semaphorin-5A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Semaphorin-5A

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