SMTL ID : 3edh.1

Crystal structure of bone morphogenetic protein 1 protease domain in complex with partially bound DMSO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.1: 8 residues within 4Å: Chain A: A.1, A.2, E.104, R.107, V.137, S.139, Q.192 Ligands: ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.107, A:V.137 Hydrogen bonds: A:R.107, A:Q.192 Water bridges: A:A.1

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.93, H.97, H.103 Ligands: DMS.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.93, A:H.97, A:H.103, DMS.6 ZN.3: 4 residues within 4Å: Chain A: A.1, E.104, Q.192 Ligands: ACE.1 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.104, A:E.104, H2O.1, H2O.1, ACE.1

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 2 residues within 4Å: Chain A: K.40, H.41 No protein-ligand interaction detected (PLIP) DMS.5: 2 residues within 4Å: Chain A: R.36, K.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.36, A:K.40 DMS.6: 6 residues within 4Å: Chain A: C.65, H.93, E.94, H.97, H.103 Ligands: ZN.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.94 DMS.7: 3 residues within 4Å: Chain A: Q.181, R.182, T.183 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.182 DMS.8: 6 residues within 4Å: Chain A: F.17, R.32, M.35, R.36, E.39, F.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.32 Salt bridges: A:E.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mac Sweeney, A. et al., Structural basis for the substrate specificity of bone morphogenetic protein 1/tolloid-like metalloproteases. To be Published

Release Date

2008-09-16

Peptides

Bone morphogenetic protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bone morphogenetic protein 1