SMTL ID : 4giq.1

Crystal Structure of mouse RANK bound to RANKL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-3-3-mer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: Y.42, H.43, D.44, R.45 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: W.47, K.49 Chain B: K.56 Chain C: F.135, K.136 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain C: Y.42, H.43, D.44, R.45 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain C: W.47, K.49 Chain D: K.56 Chain E: F.135, K.136 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain E: Y.42, H.43, D.44, R.45 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: F.135, K.136 Chain E: W.47, K.49 Chain F: K.56 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain B: C.104, A.105, P.106, F.108, S.131, V.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.108, B:S.131 NA.7: 6 residues within 4Å: Chain D: C.104, A.105, P.106, F.108, S.131, V.133 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:C.104, D:S.131 NA.11: 6 residues within 4Å: Chain F: C.104, A.105, P.106, F.108, S.131, V.133 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:A.105, F:S.131

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

NAG.4: 3 residues within 4Å: Chain B: D.73, N.76, A.79 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.79 Water bridges: B:T.78 NAG.8: 3 residues within 4Å: Chain D: D.73, N.76, A.79 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.79 Water bridges: D:T.78 NAG.12: 3 residues within 4Å: Chain F: D.73, N.76, A.79 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:A.79 Water bridges: F:T.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nelson, C.A. et al., RANKL Employs Distinct Binding Modes to Engage RANK and the Osteoprotegerin Decoy Receptor. Structure (2012)

Release Date

2012-10-24

Peptides

Tumor necrosis factor ligand superfamily member 11: ACE
Tumor necrosis factor receptor superfamily member 11A: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
R

D
R

F
R

Tumor necrosis factor ligand superfamily member 11

Tumor necrosis factor receptor superfamily member 11A

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