SMTL ID : 5bnq.1

Crystal structure of hRANKL-mRANK complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-3-mer

Ligands

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: Q.6, K.155, V.156 Chain C: Q.6, V.156 Chain E: Q.6, V.156 Ligands: PO4.14, PO4.27 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: C:Q.6, E:Q.6, A:Q.6 PO4.7: 10 residues within 4Å: Chain A: Q.80, M.82, Y.84, K.100 Chain B: K.95, C.123, E.124 Chain E: F.113, F.115, D.143 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 3 interactions with chain A Salt bridges: B:K.95, A:K.100 Hydrogen bonds: E:D.143, A:Q.80, A:Y.84 PO4.8: 4 residues within 4Å: Chain B: L.97, C.111, W.119, N.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.111, B:W.119, B:N.145 PO4.9: 8 residues within 4Å: Chain B: A.115, G.116, Y.117, N.129, L.142, Q.143, L.144, K.146 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.116, B:N.129, B:Q.143 Water bridges: B:N.145, B:N.145 PO4.14: 9 residues within 4Å: Chain A: Q.6, V.156 Chain C: Q.6, K.155, V.156 Chain E: Q.6, V.156 Ligands: PO4.1, PO4.27 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: C:Q.6, E:Q.6, A:Q.6 PO4.20: 10 residues within 4Å: Chain A: F.113, F.115, D.143 Chain C: Q.80, M.82, Y.84, K.100 Chain D: K.95, C.123, E.124 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:Q.80, C:Y.84, A:D.143 Salt bridges: C:K.100, D:K.95 PO4.21: 4 residues within 4Å: Chain D: L.97, C.111, W.119, N.145 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:C.111, D:W.119, D:N.145 PO4.22: 8 residues within 4Å: Chain D: A.115, G.116, Y.117, N.129, L.142, Q.143, L.144, K.146 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.116, D:N.129, D:Q.143 Water bridges: D:N.145, D:N.145 PO4.27: 9 residues within 4Å: Chain A: Q.6, V.156 Chain C: Q.6, V.156 Chain E: Q.6, K.155, V.156 Ligands: PO4.1, PO4.14 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: C:Q.6, E:Q.6, A:Q.6 PO4.33: 10 residues within 4Å: Chain C: F.113, F.115, D.143 Chain E: Q.80, M.82, Y.84, K.100 Chain F: K.95, C.123, E.124 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: E:Q.80, E:Y.84, C:D.143 Salt bridges: E:K.100, F:K.95 PO4.34: 4 residues within 4Å: Chain F: L.97, C.111, W.119, N.145 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:C.111, F:W.119, F:N.145 PO4.35: 8 residues within 4Å: Chain F: A.115, G.116, Y.117, N.129, L.142, Q.143, L.144, K.146 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.116, F:N.129, F:Q.143 Water bridges: F:N.145, F:N.145

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

CL.2: 8 residues within 4Å: Chain A: K.105, Y.116 Chain C: K.105, Y.116 Chain E: K.105, Y.116 Ligands: CL.15, CL.28 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: W.107, H.114 Chain C: T.104 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: F.124, K.125 Chain B: K.84 Chain E: K.38 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: Y.31, H.32, D.33, R.34 Ligand excluded by PLIP CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: Y.75, H.88, K.89, P.108, R.109 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: H.118, N.120 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain E: D.145 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain A: K.105, Y.116 Chain C: K.105, Y.116 Chain E: K.105, Y.116 Ligands: CL.2, CL.28 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: W.107, H.114 Chain E: T.104 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: K.38 Chain C: F.124, K.125 Chain D: K.84 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: Y.31, H.32, D.33, R.34 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain D: Y.75, H.88, K.89, P.108, R.109 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain D: H.118, N.120 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain A: D.145 Ligand excluded by PLIP CL.28: 8 residues within 4Å: Chain A: K.105, Y.116 Chain C: K.105, Y.116 Chain E: K.105, Y.116 Ligands: CL.2, CL.15 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain A: T.104 Chain E: W.107, H.114 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain C: K.38 Chain E: F.124, K.125 Chain F: K.84 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain E: Y.31, H.32, D.33, R.34 Ligand excluded by PLIP CL.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain F: Y.75, H.88, K.89, P.108, R.109 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain F: H.118, N.120 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain C: D.145 Ligand excluded by PLIP

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

NA.10: 5 residues within 4Å: Chain B: C.132, A.133, F.136, S.159, V.161 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.136, B:S.159, B:S.163 NA.23: 5 residues within 4Å: Chain D: C.132, A.133, F.136, S.159, V.161 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.159, D:V.161, D:S.163 NA.36: 5 residues within 4Å: Chain F: C.132, A.133, F.136, S.159, V.161 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:C.132, F:S.159, F:S.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., A RANKL mutant used as an inter-species vaccine for efficient immunotherapy of osteoporosis. Sci Rep (2015)

Release Date

2015-10-14

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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