SMTL ID : 9dpx.1

BMP-9 G389S K357R Dimer in Acidic pH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: P.81, I.82, S.83, Y.97, H.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.83, A:Y.97, A:Y.97 GOL.2: 11 residues within 4Å: Chain A: Q.58, S.70, K.71, A.72, C.73, R.110 Chain B: C.37, R.38, C.74, V.75, P.76 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:C.37, A:Q.58, A:R.110 Water bridges: B:C.37, A:S.70 GOL.12: 5 residues within 4Å: Chain B: P.81, I.82, S.83, Y.97, H.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.83, B:Y.97, B:Y.97 GOL.13: 11 residues within 4Å: Chain A: C.37, R.38, C.74, V.75, P.76 Chain B: Q.58, S.70, K.71, A.72, C.73, R.110 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.58, B:R.110, A:C.37 Water bridges: B:S.70, A:C.37

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

CL.3: 5 residues within 4Å: Chain A: K.96, H.98, Y.99, E.100 Chain B: K.53 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: T.52, K.53 Chain B: E.100, G.101 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: F.43, P.44, L.45 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Ligands: NA.10 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: F.42, P.44 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: R.14, Y.32, E.33 Ligands: NA.11 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: K.53 Chain B: K.96, H.98, Y.99, E.100 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: E.100, G.101 Chain B: T.52, K.53 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: F.43, P.44, L.45 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Ligands: NA.21 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: F.42, P.44 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: R.14, Y.32, E.33 Ligands: NA.22 Ligand excluded by PLIP

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

NA.9: 4 residues within 4Å: Chain A: F.65, P.66, T.67, K.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.65, A:T.67, A:K.68 NA.10: 6 residues within 4Å: Chain A: L.13, R.14, V.15 Chain B: V.61, F.65 Ligands: CL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14 Water bridges: A:D.19 NA.11: 3 residues within 4Å: Chain A: Y.32, E.33 Ligands: CL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.33 NA.20: 4 residues within 4Å: Chain B: F.65, P.66, T.67, K.68 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.67, B:T.67, B:T.67, B:K.68 NA.21: 6 residues within 4Å: Chain A: V.61, F.65 Chain B: L.13, R.14, V.15 Ligands: CL.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.14 NA.22: 3 residues within 4Å: Chain B: Y.32, E.33 Ligands: CL.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.33 Water bridges: B:E.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwartze, T.A. et al., Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10. J.Mol.Biol. (2025)

Release Date

2025-03-05

Peptides

Growth/differentiation factor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Growth/differentiation factor 2

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