SMTL ID : 4jph.1 (1 other biounit)

Crystal structure of Protein Related to DAN and Cerberus (PRDC)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: E.38 Chain B: P.57, L.58, R.59, L.73 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.59, A:E.38 GOL.2: 6 residues within 4Å: Chain A: H.26, H.27, I.29, F.97, S.99, S.139 No protein-ligand interaction detected (PLIP) GOL.3: 5 residues within 4Å: Chain A: S.35, R.88, H.89, K.91, D.95 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.35, A:S.35, A:R.88, A:H.89, A:K.91 Water bridges: A:R.88, A:D.95 GOL.4: 4 residues within 4Å: Chain A: R.136, C.137, M.138, S.139 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.139 GOL.5: 3 residues within 4Å: Chain A: E.64, L.120, R.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.64, A:R.125 Water bridges: A:E.64 GOL.8: 3 residues within 4Å: Chain B: H.134, C.135, R.136 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.136 Water bridges: B:C.135 GOL.9: 6 residues within 4Å: Chain B: L.40, E.44, F.84, F.97, Q.98, S.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.44, B:Q.98, B:Q.98 GOL.10: 2 residues within 4Å: Chain B: P.123, F.124 No protein-ligand interaction detected (PLIP)

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.6: 10 residues within 4Å: Chain A: Y.85, Q.98, C.100, F.102, V.140 Chain B: F.102, K.104, P.105, Q.130 Ligands: GSH.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.85, A:Q.98 GSH.11: 5 residues within 4Å: Chain A: F.102, K.104 Chain B: Q.98, C.100 Ligands: GSH.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.98 Hydrophobic interactions: A:F.102

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.7: 3 residues within 4Å: Chain B: R.75, R.107, K.133 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.133 Salt bridges: B:R.75, B:R.107, B:R.107, B:K.133, B:K.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nolan, K. et al., Structure of protein related to dan and cerberus: insights into the mechanism of bone morphogenetic protein antagonism. Structure (2013)

Release Date

2013-07-24

Peptides

Gremlin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gremlin-2

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