SMTL ID : 5o0o.1

Deglycosylated Nogo Receptor with native disulfide structure 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: A.34, S.35, S.56, R.58, N.59 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: A.131, A.132, N.156 Chain H: H.197 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.214 Ligands: GOL.4 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: A.34, S.56, N.59 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: A.131, N.156 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.214 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: A.34, S.35, S.56, N.59 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: A.131, A.132, N.156 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: N.189, H.190, A.212, N.213, N.214 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain D: A.34, S.35, S.56, N.59 Ligand excluded by PLIP NAG.54: 6 residues within 4Å: Chain A: E.172, H.197, R.200 Chain D: A.131, A.132, N.156 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain D: N.214 Ligands: GOL.56 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain E: A.34, S.35, S.56, N.59 Ligand excluded by PLIP NAG.67: 5 residues within 4Å: Chain C: E.172, H.197 Chain E: A.131, A.132, N.156 Ligand excluded by PLIP NAG.68: 1 residues within 4Å: Chain E: N.214 Ligand excluded by PLIP NAG.80: 4 residues within 4Å: Chain F: A.34, S.35, S.56, N.59 Ligand excluded by PLIP NAG.81: 3 residues within 4Å: Chain F: A.131, A.132, N.156 Ligand excluded by PLIP NAG.82: 2 residues within 4Å: Chain F: N.214 Ligands: GOL.83 Ligand excluded by PLIP NAG.97: 4 residues within 4Å: Chain G: A.34, S.35, S.56, N.59 Ligand excluded by PLIP NAG.98: 6 residues within 4Å: Chain F: E.172, H.197, R.200 Chain G: A.131, A.132, N.156 Ligand excluded by PLIP NAG.99: 1 residues within 4Å: Chain G: N.214 Ligand excluded by PLIP NAG.112: 5 residues within 4Å: Chain H: A.34, S.35, S.56, N.59 Ligands: CL.125 Ligand excluded by PLIP NAG.113: 4 residues within 4Å: Chain B: E.172, H.197 Chain H: A.131, N.156 Ligand excluded by PLIP NAG.114: 2 residues within 4Å: Chain H: N.214 Ligands: GOL.115 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Q.188, N.189, H.190, A.212, N.213, N.214 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.190, A:N.214, A:N.214 Water bridges: A:Q.188 GOL.5: 6 residues within 4Å: Chain A: M.224, W.251, K.254, F.255 Chain D: Q.230 Ligands: CL.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:W.251, A:K.254, D:Q.230 GOL.6: 7 residues within 4Å: Chain A: Y.135, H.159, F.161, R.183 Chain H: R.246, C.312 Ligands: CL.118 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain H Hydrogen bonds: A:Y.135, A:H.159, A:R.183, H:R.246 GOL.22: 5 residues within 4Å: Chain B: M.224, W.251, K.254, F.255 Chain H: Q.230 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:W.251, B:W.251, B:K.254, B:K.254, H:Q.230 GOL.56: 7 residues within 4Å: Chain D: Q.188, N.189, H.190, A.212, N.213, N.214 Ligands: NAG.55 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.190, D:N.214, D:N.214 Water bridges: D:Q.188 GOL.83: 7 residues within 4Å: Chain F: Q.188, N.189, H.190, A.212, N.213, N.214 Ligands: NAG.82 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.214 Water bridges: F:Q.188, F:N.213, F:D.236 GOL.115: 7 residues within 4Å: Chain H: Q.188, N.189, H.190, A.212, N.213, N.214 Ligands: NAG.114 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.214 Water bridges: H:Q.188

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

CL.7: 3 residues within 4Å: Chain A: R.116, Q.139, H.163 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: F.211, R.233, L.234, N.235, S.260 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: R.244, A.289, L.309 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: Q.26, R.45 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: R.38, T.61, I.62 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: F.255, R.256 Chain D: R.256 Ligands: GOL.5 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: R.273, D.274, R.277 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: T.302, D.303 Chain D: H.42 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: H.173, R.176 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: K.276, R.277 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain A: Q.139, F.161, L.162, H.163, L.185, H.187 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: P.219, A.220, E.221, P.247 Chain D: M.206 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: R.116, Q.139, H.163 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain B: Q.22, H.42, G.43, H.66, S.67 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain B: F.211, R.233, L.234, N.235, S.260 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: R.273, D.274, R.277 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: P.267, Q.268, R.269 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: N.235, S.260, E.261 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain B: Q.26, R.45 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain B: H.48, V.49, P.50, R.72, D.74 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain B: K.311 Chain H: Q.86, H.110, T.111 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain B: P.219, A.220, E.221, P.247 Chain H: M.206 Ligand excluded by PLIP CL.33: 6 residues within 4Å: Chain B: Q.139, F.161, L.162, H.163, L.185, H.187 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain B: D.182, R.183, M.206, T.207 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: R.204 Chain D: M.224, P.225 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain C: R.116, Q.139, H.163 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain C: T.302, D.303 Chain E: H.42 Ligand excluded by PLIP CL.41: 5 residues within 4Å: Chain C: F.211, R.233, L.234, N.235, S.260 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain C: F.255, R.256 Chain E: R.256 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain C: P.310, K.311, C.312 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain C: R.204 Chain G: M.224, P.225 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain C: R.273, D.274, R.277 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain C: R.244, A.289, L.309 Ligand excluded by PLIP CL.47: 4 residues within 4Å: Chain C: Q.22, H.42, G.43, H.66 Ligand excluded by PLIP CL.48: 4 residues within 4Å: Chain C: W.251, K.254, F.255 Chain E: Q.230 Ligand excluded by PLIP CL.49: 5 residues within 4Å: Chain C: Q.139, F.161, H.163, L.185, H.187 Ligand excluded by PLIP CL.50: 5 residues within 4Å: Chain C: P.219, A.220, E.221, P.247 Chain E: M.206 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain C: R.38, T.61, I.62 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain C: Y.11, N.12, E.13 Ligand excluded by PLIP CL.57: 3 residues within 4Å: Chain D: R.116, Q.139, H.163 Ligand excluded by PLIP CL.58: 5 residues within 4Å: Chain D: F.211, R.233, L.234, N.235, S.260 Ligand excluded by PLIP CL.59: 5 residues within 4Å: Chain D: H.48, V.49, P.50, R.72, D.74 Ligand excluded by PLIP CL.60: 4 residues within 4Å: Chain D: D.182, R.183, M.206, T.207 Ligand excluded by PLIP CL.61: 3 residues within 4Å: Chain A: K.254 Chain D: F.255, R.256 Ligand excluded by PLIP CL.62: 4 residues within 4Å: Chain D: Q.22, H.42, G.43, H.66 Ligand excluded by PLIP CL.63: 4 residues within 4Å: Chain D: P.219, A.220, E.221, P.247 Ligand excluded by PLIP CL.64: 6 residues within 4Å: Chain D: Q.139, F.161, L.162, H.163, L.185, H.187 Ligand excluded by PLIP CL.65: 4 residues within 4Å: Chain A: M.224, P.225 Chain D: R.204, R.227 Ligand excluded by PLIP CL.69: 3 residues within 4Å: Chain E: R.116, Q.139, H.163 Ligand excluded by PLIP CL.70: 5 residues within 4Å: Chain E: Q.22, H.42, G.43, H.66, S.67 Ligand excluded by PLIP CL.71: 4 residues within 4Å: Chain E: D.182, R.183, M.206, T.207 Ligand excluded by PLIP CL.72: 3 residues within 4Å: Chain E: R.273, D.274, R.277 Ligand excluded by PLIP CL.73: 2 residues within 4Å: Chain E: K.311, C.312 Ligand excluded by PLIP CL.74: 5 residues within 4Å: Chain E: H.48, V.49, P.50, R.72, D.74 Ligand excluded by PLIP CL.75: 5 residues within 4Å: Chain E: F.211, R.233, L.234, N.235, S.260 Ligand excluded by PLIP CL.76: 6 residues within 4Å: Chain E: Q.139, F.161, L.162, H.163, L.185, H.187 Ligand excluded by PLIP CL.77: 3 residues within 4Å: Chain E: P.267, Q.268, R.269 Ligand excluded by PLIP CL.78: 4 residues within 4Å: Chain E: P.219, A.220, E.221, P.247 Ligand excluded by PLIP CL.79: 3 residues within 4Å: Chain E: V.170, R.193, H.195 Ligand excluded by PLIP CL.84: 3 residues within 4Å: Chain F: R.116, Q.139, H.163 Ligand excluded by PLIP CL.85: 4 residues within 4Å: Chain F: Q.22, H.42, G.43, H.66 Ligand excluded by PLIP CL.86: 5 residues within 4Å: Chain F: F.211, R.233, L.234, N.235, S.260 Ligand excluded by PLIP CL.87: 2 residues within 4Å: Chain F: Q.26, R.45 Ligand excluded by PLIP CL.88: 5 residues within 4Å: Chain F: H.48, V.49, P.50, R.72, D.74 Ligand excluded by PLIP CL.89: 5 residues within 4Å: Chain F: P.219, A.220, E.221, P.247 Chain G: M.206 Ligand excluded by PLIP CL.90: 3 residues within 4Å: Chain F: N.235, S.260, E.261 Ligand excluded by PLIP CL.91: 3 residues within 4Å: Chain F: R.38, T.61, I.62 Ligand excluded by PLIP CL.92: 3 residues within 4Å: Chain F: M.224, P.225 Chain G: R.204 Ligand excluded by PLIP CL.93: 3 residues within 4Å: Chain F: R.273, D.274, R.277 Ligand excluded by PLIP CL.94: 6 residues within 4Å: Chain F: Q.139, F.161, L.162, H.163, L.185, H.187 Ligand excluded by PLIP CL.95: 2 residues within 4Å: Chain F: R.244, L.309 Ligand excluded by PLIP CL.96: 3 residues within 4Å: Chain F: P.171, E.172, H.195 Ligand excluded by PLIP CL.100: 3 residues within 4Å: Chain G: R.116, Q.139, H.163 Ligand excluded by PLIP CL.101: 5 residues within 4Å: Chain C: F.40, H.42 Chain G: T.302, D.303, E.304 Ligand excluded by PLIP CL.102: 5 residues within 4Å: Chain G: Q.22, H.42, G.43, H.66, S.67 Ligand excluded by PLIP CL.103: 5 residues within 4Å: Chain G: F.211, R.233, L.234, N.235, S.260 Ligand excluded by PLIP CL.104: 5 residues within 4Å: Chain G: H.48, V.49, P.50, R.72, D.74 Ligand excluded by PLIP CL.105: 3 residues within 4Å: Chain G: H.197, R.200, P.225 Ligand excluded by PLIP CL.106: 3 residues within 4Å: Chain G: P.267, Q.268, R.269 Ligand excluded by PLIP CL.107: 2 residues within 4Å: Chain G: R.273, D.274 Ligand excluded by PLIP CL.108: 4 residues within 4Å: Chain G: R.244, A.287, V.288, A.289 Ligand excluded by PLIP CL.109: 1 residues within 4Å: Chain G: H.187 Ligand excluded by PLIP CL.110: 4 residues within 4Å: Chain G: P.219, A.220, E.221, P.247 Ligand excluded by PLIP CL.111: 6 residues within 4Å: Chain G: Q.139, F.161, L.162, H.163, L.185, H.187 Ligand excluded by PLIP CL.116: 4 residues within 4Å: Chain H: F.211, R.233, N.235, S.260 Ligand excluded by PLIP CL.117: 3 residues within 4Å: Chain H: R.273, D.274, R.277 Ligand excluded by PLIP CL.118: 4 residues within 4Å: Chain H: P.310, K.311, C.312 Ligands: GOL.6 Ligand excluded by PLIP CL.119: 5 residues within 4Å: Chain H: H.48, V.49, P.50, R.72, D.74 Ligand excluded by PLIP CL.120: 3 residues within 4Å: Chain H: R.116, Q.139, H.163 Ligand excluded by PLIP CL.121: 4 residues within 4Å: Chain H: Q.22, H.42, G.43, H.66 Ligand excluded by PLIP CL.122: 4 residues within 4Å: Chain H: D.182, R.183, M.206, T.207 Ligand excluded by PLIP CL.123: 4 residues within 4Å: Chain H: P.219, A.220, E.221, P.247 Ligand excluded by PLIP CL.124: 6 residues within 4Å: Chain H: Q.139, F.161, L.162, H.163, L.185, H.187 Ligand excluded by PLIP CL.125: 3 residues within 4Å: Chain H: S.35, N.59 Ligands: NAG.112 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pronker, M.F. et al., Nogo Receptor crystal structures with a native disulfide pattern suggest a novel mode of self-interaction. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-10-18

Peptides

Reticulon-4 receptor: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Reticulon-4 receptor

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