SMTL ID : 4nzd.4 (3 other biounits)

Interleukin 21 receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-hexamer

Ligands

6 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.1: 8 residues within 4Å: Chain A: A.52, H.53, N.54, H.57, T.59 Chain D: V.5, I.17 Ligands: MAN.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:A.52, D:V.5, D:I.17 Hydrogen bonds: A:T.59 NAG-NAG-BMA-MAN-FUC.12: 8 residues within 4Å: Chain B: A.52, H.53, N.54, H.57, T.59 Chain F: V.5, I.17 Ligands: MAN.13 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:A.52, F:V.5, F:I.17 Hydrogen bonds: B:T.59 NAG-NAG-BMA-MAN-FUC.23: 9 residues within 4Å: Chain C: V.5, I.17, N.54, H.57, T.59, R.154 Ligands: MAN.25, CL.28, CL.29 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.59, C:R.154, C:R.154 Hydrophobic interactions: C:V.5, C:I.17 NAG-NAG-BMA-MAN-FUC.24: 6 residues within 4Å: Chain B: I.17 Chain D: N.54, H.57, T.59 Ligands: MAN.32, EDO.37 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:T.59, D:T.59 Water bridges: D:N.54 Hydrophobic interactions: B:I.17 NAG-NAG-BMA-MAN-FUC.38: 9 residues within 4Å: Chain E: V.5, I.17, N.54, H.57, T.59, R.154 Ligands: MAN.40, CL.43, CL.44 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.154, E:R.154 Hydrophobic interactions: E:V.5, E:I.17 NAG-NAG-BMA-MAN-FUC.39: 6 residues within 4Å: Chain A: I.17 Chain F: N.54, H.57, T.59 Ligands: MAN.47, EDO.52 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:T.59 Water bridges: F:N.54 Hydrophobic interactions: A:I.17

6 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.2: 6 residues within 4Å: Chain A: R.182, T.194, W.195 Ligands: NAG-NAG-BMA-MAN-FUC.1, NAG-NAG-BMA-MAN-FUC.1, CL.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.182, A:R.182, A:T.194, A:T.194, A:W.195, A:W.195 MAN.13: 6 residues within 4Å: Chain B: R.182, T.194, W.195 Ligands: NAG-NAG-BMA-MAN-FUC.12, NAG-NAG-BMA-MAN-FUC.12, CL.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.182, B:R.182, B:T.194, B:W.195, B:W.195 MAN.25: 5 residues within 4Å: Chain C: R.182, T.194, W.195 Ligands: NAG-NAG-BMA-MAN-FUC.23, NAG-NAG-BMA-MAN-FUC.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.182, C:R.182, C:W.195, C:W.195 MAN.32: 5 residues within 4Å: Chain D: R.182, T.194, W.195 Ligands: NAG-NAG-BMA-MAN-FUC.24, CL.35 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.182, D:R.182, D:T.194, D:T.194, D:W.195, D:W.195 Water bridges: D:R.154 MAN.40: 5 residues within 4Å: Chain E: R.182, T.194, W.195 Ligands: NAG-NAG-BMA-MAN-FUC.38, NAG-NAG-BMA-MAN-FUC.38 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.182, E:R.182, E:W.195, E:W.195 MAN.47: 5 residues within 4Å: Chain F: R.182, T.194, W.195 Ligands: NAG-NAG-BMA-MAN-FUC.39, CL.50 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.182, F:R.182, F:T.194, F:W.195, F:W.195 Water bridges: F:R.154

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

NA.3: 3 residues within 4Å: Chain A: Y.123, Y.137, D.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.137, A:D.160 NA.4: 1 residues within 4Å: Chain A: G.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.193 NA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.14: 3 residues within 4Å: Chain B: Y.123, Y.137, D.160 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.160 NA.15: 1 residues within 4Å: Chain B: G.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.193 NA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.33: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.84 NA.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.48: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.84 NA.49: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.6: 2 residues within 4Å: Chain A: P.185 Ligands: MAN.2 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: D.160 Chain F: Q.88 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: S.87, Q.88 Chain C: G.133, K.134 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: P.185 Ligands: MAN.13 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: D.160 Chain D: Q.88 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: S.87, Q.88 Chain E: G.133, K.134 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain C: Q.136, G.184, P.185, W.195 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain C: H.24 Chain D: Q.116 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-FUC.23 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain C: K.100 Ligands: NAG-NAG-BMA-MAN-FUC.23 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain C: Y.137, D.160 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Ligands: MAN.32 Ligand excluded by PLIP CL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain E: Q.136, G.184, P.185, W.195 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain E: H.24 Chain F: Q.116 Ligand excluded by PLIP CL.43: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-FUC.38 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain E: K.100 Ligands: NAG-NAG-BMA-MAN-FUC.38 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain E: Y.137, D.160 Ligand excluded by PLIP CL.50: 1 residues within 4Å: Ligands: MAN.47 Ligand excluded by PLIP CL.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

6 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.10: 10 residues within 4Å: Chain A: K.100, P.101, A.102, P.103, E.197 Chain D: Y.7, T.8, D.9, T.13, I.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.100 Salt bridges: A:K.100 TLA.11: 6 residues within 4Å: Chain A: D.9, T.13, I.15 Chain F: K.100, P.101, A.102 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:P.101, A:T.13 Water bridges: F:K.100, A:T.13 TLA.21: 10 residues within 4Å: Chain B: K.100, P.101, A.102, P.103, E.197 Chain F: Y.7, T.8, D.9, T.13, I.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:K.100 Salt bridges: B:K.100 Water bridges: F:D.9 TLA.22: 6 residues within 4Å: Chain B: D.9, T.13, I.15 Chain D: K.100, P.101, A.102 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:P.101, B:D.9, B:T.13 Water bridges: D:K.100 TLA.31: 6 residues within 4Å: Chain C: D.9, T.13, I.15, K.100, P.101, P.103 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.9, C:D.9 Water bridges: C:K.100, C:P.101, C:D.122 Salt bridges: C:K.100 TLA.46: 6 residues within 4Å: Chain E: D.9, T.13, I.15, K.100, P.101, P.103 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.9, E:T.13 Water bridges: E:K.100, E:P.101 Salt bridges: E:K.100

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

EDO.37: 3 residues within 4Å: Chain B: D.3, E.19 Ligands: NAG-NAG-BMA-MAN-FUC.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.3, B:D.3 EDO.52: 3 residues within 4Å: Chain A: D.3, E.19 Ligands: NAG-NAG-BMA-MAN-FUC.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamming, O.T. et al., Interleukin 21 receptor structure and function. To be Published

Release Date

2014-12-17

Peptides

Interleukin-21 receptor: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
C

E
B

F
C

Interleukin-21 receptor

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