SMTL ID : 4y5v.1 (1 other biounit)

Diabody 305 complex with EpoR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-oligomer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: S.113, D.114, W.115 Chain B: P.47, K.48 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.114, A:W.115, B:P.47 GOL.2: 6 residues within 4Å: Chain A: G.49 Chain B: Q.41, H.42, P.43, G.44, K.45 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.44, B:K.45, B:K.45, A:G.49 GOL.3: 9 residues within 4Å: Chain B: I.34, D.53, R.56 Chain C: L.31, E.32, T.85, A.86, T.88, S.89 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.56, C:T.88, C:S.89 Water bridges: B:D.53, B:S.55 GOL.4: 7 residues within 4Å: Chain A: G.49, K.50, G.51 Chain B: D.88, Y.90, G.104, G.105 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.50, B:D.88, B:G.105 Water bridges: B:Y.90 GOL.5: 6 residues within 4Å: Chain D: D.61, G.62, R.79, D.80, N.81 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.80, D:D.80, D:N.81 Water bridges: D:N.81 GOL.6: 6 residues within 4Å: Chain D: I.58, G.62, K.65, S.78, R.79 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.65, D:R.79 GOL.9: 6 residues within 4Å: Chain D: Q.46, G.49, K.50 Chain E: Q.41, G.44, K.45 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:G.44, E:K.45, D:Q.46, D:G.49, D:K.50, D:Y.102, D:Y.102 Water bridges: E:Q.41 GOL.10: 7 residues within 4Å: Chain E: I.34, D.53, R.56 Chain F: E.32, T.85, T.88, S.89 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:D.53, F:T.88, F:T.88, F:S.89 GOL.11: 8 residues within 4Å: Chain D: G.49, K.50 Chain E: D.88, Y.90, G.104, G.105, T.106, K.107 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:D.88, E:Y.90, E:G.105 Water bridges: D:Q.46 GOL.12: 2 residues within 4Å: Chain F: R.189, S.215 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.189, F:S.215

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 6 residues within 4Å: Chain D: G.62, S.63, E.64, K.65, Y.67, T.76 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.65, D:Y.67 Water bridges: D:T.76

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 3 residues within 4Å: Chain D: G.17, L.120, T.122 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moraga, I. et al., Tuning Cytokine Receptor Signaling by Re-orienting Dimer Geometry with Surrogate Ligands. Cell (2015)

Release Date

2015-04-29

Peptides

diabody 305 VH domain: AD
Diabody 305 VL domain: BE
Erythropoietin receptor: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

diabody 305 VH domain

Diabody 305 VL domain

Erythropoietin receptor

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