SMTL ID : 9dpo.1

BMP-9 Wild-Type Dimer With Radiation Damage in Neutral pH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 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: 4 residues within 4Å: Chain A: T.52, K.53 Chain B: L.79, G.101 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: F.43, P.44, L.45 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: K.96, Y.97, H.98 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: Y.97, H.98 Ligands: NA.6 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: K.53 Chain B: K.96, H.98, Y.99, E.100 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: L.79, G.101 Chain B: T.52, K.53 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: F.43, P.44, L.45 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: Y.97, H.98 Ligands: NA.16 Ligand excluded by PLIP

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

NA.6: 3 residues within 4Å: Chain A: Y.97, H.98 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.97, A:Y.97 NA.7: 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.8: 7 residues within 4Å: Chain A: R.14, V.15, N.16, D.19 Chain B: V.61, F.65 Ligands: NA.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.14, A:N.16, A:D.19 NA.9: 3 residues within 4Å: Chain A: R.14, N.16 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.14 NA.16: 3 residues within 4Å: Chain B: Y.97, H.98 Ligands: CL.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.97, B:Y.97 NA.17: 4 residues within 4Å: Chain B: F.65, P.66, T.67, K.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.67, B:T.67 NA.18: 7 residues within 4Å: Chain A: V.61, F.65 Chain B: R.14, V.15, N.16, D.19 Ligands: NA.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.16, B:D.19 NA.19: 3 residues within 4Å: Chain B: R.14, N.16 Ligands: NA.18 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: P.81, I.82, S.83, Y.97, H.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.97, A:H.98 GOL.20: 5 residues within 4Å: Chain B: P.81, I.82, S.83, Y.97, H.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.97, B:H.98

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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