SMTL ID : 8ckk.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

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

MAN.1: 5 residues within 4Å: Chain A: F.7, W.8, R.30, A.39 Ligands: NO3.5 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.8, A:W.8, A:R.30, A:R.30 Water bridges: B:D.37 MAN.11: 3 residues within 4Å: Chain A: G.10, W.11, R.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.11, A:W.11, A:R.28, A:R.28 MAN.20: 3 residues within 4Å: Chain B: G.10, W.11, R.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.11, B:W.11, B:R.28, B:R.28 MAN.21: 4 residues within 4Å: Chain B: F.7, W.8, R.30, A.39 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.8, B:W.8, B:R.30, B:R.30 Water bridges: B:A.39

17 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 4 residues within 4Å: Chain A: C.41, N.42, V.43 Chain B: C.41 Ligand excluded by PLIP NO3.3: 9 residues within 4Å: Chain A: Y.106, C.107, S.108, D.110, G.111, T.112, S.113, G.114, C.115 Ligand excluded by PLIP NO3.4: 1 residues within 4Å: Chain A: H.5 Ligand excluded by PLIP NO3.5: 4 residues within 4Å: Chain A: M.6, C.38, A.39 Ligands: MAN.1 Ligand excluded by PLIP NO3.6: 5 residues within 4Å: Chain A: A.19, Q.20, C.21, A.90 Ligands: NO3.10 Ligand excluded by PLIP NO3.7: 5 residues within 4Å: Chain A: G.22, P.52, C.53, R.88 Chain B: L.94 Ligand excluded by PLIP NO3.8: 3 residues within 4Å: Chain A: C.32, P.36, N.42 Ligand excluded by PLIP NO3.9: 4 residues within 4Å: Chain A: T.59, R.82, T.84 Chain B: R.101 Ligand excluded by PLIP NO3.10: 5 residues within 4Å: Chain A: L.89, A.90, D.91, L.94 Ligands: NO3.6 Ligand excluded by PLIP NO3.12: 7 residues within 4Å: Chain A: G.98, R.99, R.101 Chain B: K.57, T.84, K.86 Ligands: NO3.16 Ligand excluded by PLIP NO3.13: 6 residues within 4Å: Chain A: K.57, T.84, K.86 Chain B: G.98, R.99, R.101 Ligand excluded by PLIP NO3.14: 4 residues within 4Å: Chain B: A.19, Q.20, C.21, A.90 Ligand excluded by PLIP NO3.15: 8 residues within 4Å: Chain B: Y.106, C.107, S.108, G.111, T.112, S.113, G.114, C.115 Ligand excluded by PLIP NO3.16: 5 residues within 4Å: Chain A: R.101 Chain B: T.59, R.82, T.84 Ligands: NO3.12 Ligand excluded by PLIP NO3.17: 6 residues within 4Å: Chain A: G.40, C.41 Chain B: W.8, G.40, C.41, N.42 Ligand excluded by PLIP NO3.18: 2 residues within 4Å: Chain B: P.4, N.34 Ligand excluded by PLIP NO3.19: 2 residues within 4Å: Chain B: P.61, W.62 Ligand excluded by PLIP

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

Related Entries With Identical Sequence