SMTL ID : 8ckg.1

Semaphorin-5A TSR 3-4 domains in complex with sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: G.98, R.99, R.101 Chain B: T.84 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.84, A:R.99 Salt bridges: B:K.57, B:K.86, A:R.99, A:R.101 Water bridges: A:R.101, A:R.101 SO4.4: 5 residues within 4Å: Chain A: T.84, K.86 Chain B: G.98, R.99, R.101 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.99, A:T.84 Salt bridges: B:R.99, B:R.101, A:K.86

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

MAN.2: 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.3: 3 residues within 4Å: Chain A: G.10, W.11, R.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.9, A:W.11, A:R.28, A:R.28 MAN.5: 5 residues within 4Å: Chain B: F.7, W.8, R.30, C.38, 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.6: 3 residues within 4Å: Chain B: G.10, W.11, R.28 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.11, B:W.11, B:R.28, B:R.28 Water bridges: B:R.30

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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