SMTL ID : 9dpt.1

BMP-9 G389S Dimer With Radiation Damage in Neutral pH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: K.96, H.98, Y.99, E.100 Chain B: K.53 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: Y.97, H.98 Ligands: NA.6 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.96, Y.97, H.98 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: F.43, P.44, L.45 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: T.50, T.52 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: K.53 Chain B: K.96, H.98, Y.99, E.100 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: Y.97, H.98 Ligands: NA.17 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: K.96, Y.97, H.98 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: F.43, P.44, L.45 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: T.50, T.52 Ligand excluded by PLIP

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

NA.6: 4 residues within 4Å: Chain A: Y.97, H.98 Ligands: CL.2, GOL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.97, A:Y.97, A:H.98 NA.7: 4 residues within 4Å: Chain A: F.65, P.66, T.67, K.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.67 NA.8: 3 residues within 4Å: Chain A: T.67, S.70 Chain B: K.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.67 NA.9: 4 residues within 4Å: Chain A: T.52, K.53 Chain B: E.100, G.101 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.53, A:K.53, B:E.100 NA.17: 4 residues within 4Å: Chain B: Y.97, H.98 Ligands: CL.13, GOL.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.97, B:H.98 NA.18: 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.19: 3 residues within 4Å: Chain A: K.38 Chain B: T.67, S.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.67 NA.20: 4 residues within 4Å: Chain A: E.100, G.101 Chain B: T.52, K.53 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.100, B:K.53, B:K.53

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: P.81, I.82, S.83, Y.97, H.98 Ligands: NA.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.83, A:Y.97, A:H.98 GOL.11: 12 residues within 4Å: Chain A: Q.58, S.70, K.71, A.72, C.73, R.110 Chain B: E.36, C.37, C.73, C.74, V.75, P.76 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.58, A:K.71, A:C.73, B:C.37, B:C.37 Water bridges: A:S.70 GOL.21: 6 residues within 4Å: Chain B: P.81, I.82, S.83, Y.97, H.98 Ligands: NA.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.83, B:Y.97, B:H.98 GOL.22: 12 residues within 4Å: Chain A: E.36, C.37, 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: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:C.37, A:C.37, B:Q.58, B:K.71, B:C.73 Water bridges: B:S.70

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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