SMTL ID : 6unp.2 (1 other biounit)

Crystal structure of the kinase domain of BMPR2-D485G

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 19 residues within 4Å: Chain A: I.43, G.44, R.45, G.46, R.47, Y.48, G.49, V.51, A.62, K.64, M.113, E.114, Y.116, S.120, R.171, N.172, L.174, D.185 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.46, A:G.46, A:R.47, A:Y.48, A:G.49, A:E.114, A:Y.116, A:S.120, A:S.120 Water bridges: A:S.120, A:S.120, A:R.171, A:N.172, A:N.172 Salt bridges: A:K.64, A:K.64

11 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.172, D.185 Ligands: ADP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.185, H2O.1, H2O.1 MG.3: 3 residues within 4Å: Chain A: P.60, E.114, Y.115 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.60, H2O.2 MG.4: 3 residues within 4Å: Chain A: K.78, N.79, R.82 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: E.77, Y.81, M.113, S.184, D.185 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.77, A:Y.81, H2O.1 MG.6: 3 residues within 4Å: Chain A: Y.124, N.177, G.179 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain A: L.125, H.128, T.129, S.130, R.253 Ligands: MG.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.130 MG.8: 4 residues within 4Å: Chain A: H.150, T.327, A.328 Ligands: MG.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.150 MG.9: 5 residues within 4Å: Chain A: S.130, S.135, I.250, R.253 Ligands: MG.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.135, A:I.250 MG.10: 3 residues within 4Å: Chain A: E.152, T.193, E.232 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.152, A:E.232 MG.11: 4 residues within 4Å: Chain A: H.150, T.151, K.236 Ligands: MG.8 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain A: I.43, Y.115 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.115, H2O.1

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 2 residues within 4Å: Chain A: H.128, T.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.129, A:T.129 Salt bridges: A:H.128 SO4.14: 7 residues within 4Å: Chain A: R.171, R.215, M.268, N.276, H.277, P.278 Ligands: EDO.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.277 Salt bridges: A:R.171, A:R.215, A:H.277

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.15: 6 residues within 4Å: Chain A: R.45, G.46, R.47, Y.48, G.49, A.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.45, A:R.45, A:R.47 EDO.16: 2 residues within 4Å: Chain A: R.171 Ligands: SO4.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.171 Water bridges: A:R.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agnew, C. et al., Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization. Nat Commun (2021)

Release Date

2021-07-07

Peptides

Bone morphogenetic protein receptor type-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bone morphogenetic protein receptor type-2

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