SMTL ID : 9dpw.1

BMP-9 K357R G389S Dimer With Radiation Damage in Neutral pH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: P.81, I.82, S.83, Y.97, H.98, Y.99 Ligands: NA.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.82, A:S.83, A:H.98 GOL.2: 12 residues within 4Å: Chain A: Q.58, S.70, K.71, A.72, C.73, R.110 Chain B: C.37, R.38, C.73, C.74, V.75, P.76 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.58, A:S.70, A:K.71, A:K.71, A:R.110 Water bridges: B:C.37 GOL.15: 7 residues within 4Å: Chain B: P.81, I.82, S.83, Y.97, H.98, Y.99 Ligands: NA.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.82, B:S.83, B:H.98 GOL.16: 12 residues within 4Å: Chain A: C.37, R.38, C.73, C.74, V.75, P.76 Chain B: Q.58, S.70, K.71, A.72, C.73, R.110 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.58, B:S.70, B:K.71, B:K.71, B:R.110 Water bridges: A:C.37

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

CL.3: 4 residues within 4Å: Chain A: K.96, Y.99, E.100 Chain B: K.53 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: T.52, K.53 Chain B: 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: 3 residues within 4Å: Chain A: K.96, Y.97, H.98 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Y.97, H.98 Ligands: NA.12 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: H.7, P.44 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: T.67, K.68, S.70 Chain B: R.38 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: L.13, R.14 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: K.53 Chain B: K.96, Y.99, E.100 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: G.101 Chain B: T.52, K.53 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: F.43, P.44, L.45 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: K.96, Y.97, H.98 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: Y.97, H.98 Ligands: NA.26 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: H.7, P.44 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: R.38 Chain B: T.67, K.68, S.70 Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: L.13, R.14 Ligand excluded by PLIP

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

NA.12: 4 residues within 4Å: Chain A: Y.97, H.98 Ligands: GOL.1, CL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.97, A:Y.97 NA.13: 4 residues within 4Å: Chain A: F.65, P.66, T.67, K.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.67, A:T.67 NA.14: 1 residues within 4Å: Chain B: K.68 No protein-ligand interaction detected (PLIP) NA.26: 4 residues within 4Å: Chain B: Y.97, H.98 Ligands: GOL.15, CL.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.97, B:H.98 NA.27: 4 residues within 4Å: Chain B: F.65, P.66, T.67, K.68 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.67 NA.28: 1 residues within 4Å: Chain A: K.68 No protein-ligand interaction detected (PLIP)

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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