SMTL ID : 7kbu.1

Structure of Hevin FS-EC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain A: N.46, C.79, K.80, S.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.81 NAG-NAG.2: 5 residues within 4Å: Chain B: N.46, C.79, K.80, S.81, R.199 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.80 Hydrogen bonds: B:S.81

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: D.170, H.172, P.173, M.174, D.175, V.177, L.178, E.182 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.170, A:P.173, A:D.175, A:E.182, H2O.3 CA.4: 6 residues within 4Å: Chain A: D.205, N.207, D.209, H.211, I.212, E.216 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.205, A:D.209, A:H.211, A:E.216, H2O.1 CA.9: 7 residues within 4Å: Chain B: D.170, H.172, P.173, D.175, V.177, L.178, E.182 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.170, B:D.175, B:E.182, B:E.182, H2O.4 CA.10: 6 residues within 4Å: Chain B: D.205, N.207, D.209, H.211, I.212, E.216 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.205, B:D.209, B:H.211, B:E.216, B:E.216 CA.11: 4 residues within 4Å: Chain B: D.87, C.220, F.221 Ligands: FMT.15 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.87, B:C.220, H2O.4, H2O.6, H2O.7 CA.12: 7 residues within 4Å: Chain A: E.89, E.194, H.195, C.196 Chain B: E.89, E.194, H.195 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.89, B:E.194, B:E.194, A:E.89, A:E.194, H2O.6

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 6 residues within 4Å: Chain A: T.84, C.85, T.198, R.199, F.200, E.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.85, A:R.199 Water bridges: A:D.87 FMT.13: 3 residues within 4Å: Chain B: N.154, Y.155, H.156 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.154, B:Y.155, B:H.156, B:H.156 FMT.14: 9 residues within 4Å: Chain A: Q.92, R.98, M.193, E.194 Chain B: I.91, Q.92, F.93, R.98 Ligands: NA.16 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.98, A:E.194, B:Q.92, B:F.93, B:R.98 FMT.15: 9 residues within 4Å: Chain B: T.84, C.85, V.90, T.198, R.199, F.200, C.204, C.220 Ligands: CA.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.199

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: F.88, H.142, P.143, I.144, D.145 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: P.94, L.95 Chain B: P.94, L.95 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: C.8, K.9, H.12, C.24 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain A: V.90, I.91, Q.92 Chain B: L.95, R.98, D.99, K.102 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.16: 6 residues within 4Å: Chain B: F.88, E.89, I.91, Q.92, F.93 Ligands: FMT.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.91, B:F.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, S. et al., Interplay between hevin, SPARC, and MDGAs: Modulators of neurexin-neuroligin transsynaptic bridges. Structure (2021)

Release Date

2021-02-10

Peptides

Proliferation-inducing protein 33: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proliferation-inducing protein 33