SMTL ID : 6z3j.1

Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: V.83, P.84, R.117 Chain B: P.84, R.117 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.84 Water bridges: B:R.117, B:R.117, B:R.117, A:R.117 Salt bridges: B:R.117, A:R.117 SO4.6: 2 residues within 4Å: Chain C: Q.4, R.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.4 Salt bridges: C:R.6

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 12 residues within 4Å: Chain A: Q.66, P.78, P.79, T.80, C.81, R.117 Chain B: C.45, E.46, C.81, C.82, V.83, P.84 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.66, A:R.117, B:C.45 Water bridges: B:C.45 GOL.4: 4 residues within 4Å: Chain B: D.96, A.98, N.100, V.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.100

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

EDO.3: 6 residues within 4Å: Chain B: E.50, F.51, R.54 Chain C: F.14, T.18, F.32 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.18, C:T.18, B:F.51, B:R.54 EDO.7: 6 residues within 4Å: Chain B: P.52, L.53, V.64 Chain C: V.55, S.58, A.59 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:L.53, C:V.55 EDO.10: 5 residues within 4Å: Chain A: F.51, P.52, L.53 Chain D: V.55, A.59 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:V.55, A:L.53

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Chain B: S.91 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain C: R.37, G.76 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain D: R.37, C.72, S.73 Ligand excluded by PLIP

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 4 residues within 4Å: Chain D: D.29, Q.69, R.70, N.71 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.69, D:N.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malinauskas, T. et al., Repulsive guidance molecules lock growth differentiation factor 5 in an inhibitory complex. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-07-01

Peptides

Growth/differentiation factor 5: AB
RGM domain family member B: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Growth/differentiation factor 5

RGM domain family member B

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