SMTL ID : 7ag0.1

Complex between the bone morphogenetic protein 2 and its antagonist Noggin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-2-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.8, P.9, P.11 Chain B: W.31, Y.91, L.92, D.93, E.94 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.94, B:E.94, A:R.8 GOL.2: 10 residues within 4Å: Chain B: Q.64, P.75, K.76, C.78, R.114 Chain D: C.43, H.44, C.78, C.79, P.81 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:C.79, B:Q.64, B:R.114 Water bridges: D:C.43 GOL.3: 7 residues within 4Å: Chain B: V.67, V.70, N.71 Chain D: Y.20, V.21, D.22, D.25 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.22, D:D.22, B:N.71 GOL.4: 4 residues within 4Å: Chain A: I.21, H.23 Chain B: Y.20, H.39 No protein-ligand interaction detected (PLIP) GOL.5: 8 residues within 4Å: Chain C: R.8, P.9, P.11 Chain D: W.31, Y.91, L.92, D.93, E.94 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.94, C:R.8 GOL.6: 10 residues within 4Å: Chain B: C.43, H.44, C.78, C.79, P.81 Chain D: Q.64, P.75, K.76, C.78, R.114 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:C.79, D:Q.64, D:R.114 Water bridges: B:C.43 GOL.7: 7 residues within 4Å: Chain B: Y.20, V.21, D.22, D.25 Chain D: V.67, V.70, N.71 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.22, B:D.22, B:D.25, D:N.71 GOL.8: 4 residues within 4Å: Chain C: I.21, H.23 Chain D: Y.20, H.39 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robert, C. et al., Structural analysis of the interaction between human cytokine BMP-2 and the antagonist Noggin reveals molecular details of cell chondrogenesis inhibition. J.Biol.Chem. (2023)

Release Date

2022-04-13

Peptides

Noggin: AC
Bone morphogenetic protein 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Noggin

Bone morphogenetic protein 2

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