SMTL ID : 2v5e.1

The structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GU4- YYJ: 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose(Non-covalent)

GU4-YYJ.1: 11 residues within 4Å: Chain A: R.41, K.45, R.48, Q.49, K.53, N.104, Y.105, I.106 Ligands: EDO.2, EDO.3, EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.104, A:Y.105, A:I.106, A:Q.49 Water bridges: A:K.45, A:R.48, A:C.107, A:K.53, A:K.53 Salt bridges: A:R.41, A:K.45, A:K.45, A:R.48, A:R.48, A:K.45, A:K.45, A:R.48, A:K.53 GU4-YYJ.7: 11 residues within 4Å: Chain C: R.41, K.45, R.48, Q.49, K.53, N.104, Y.105, I.106 Ligands: EDO.8, EDO.9, EDO.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.104, C:Y.105, C:I.106, C:Q.49 Water bridges: C:K.45, C:R.48, C:C.107, C:K.53, C:K.53 Salt bridges: C:R.41, C:K.45, C:K.45, C:R.48, C:R.48, C:K.45, C:K.45, C:R.48, C:K.53

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

EDO.2: 6 residues within 4Å: Chain A: D.52, I.106, R.110 Ligands: GU4-YYJ.1, EDO.3, EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.110, A:R.110 Water bridges: A:R.48 EDO.3: 6 residues within 4Å: Chain A: R.48, Q.49, D.52, K.53 Ligands: GU4-YYJ.1, EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.53 EDO.4: 6 residues within 4Å: Chain A: Y.105, I.106, S.109, R.110 Ligands: GU4-YYJ.1, EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.109, A:S.109, A:R.110 EDO.5: 5 residues within 4Å: Chain A: P.28, K.42, K.45, A.46, Q.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.42 Water bridges: A:Q.49 EDO.8: 6 residues within 4Å: Chain C: D.52, I.106, R.110 Ligands: GU4-YYJ.7, EDO.9, EDO.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.110, C:R.110 Water bridges: C:R.48 EDO.9: 6 residues within 4Å: Chain C: R.48, Q.49, D.52, K.53 Ligands: GU4-YYJ.7, EDO.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.52, C:K.53 EDO.10: 6 residues within 4Å: Chain C: Y.105, I.106, S.109, R.110 Ligands: GU4-YYJ.7, EDO.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.109, C:S.109, C:R.110 EDO.11: 5 residues within 4Å: Chain C: P.28, K.42, K.45, A.46, Q.49 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.42 Water bridges: C:Q.49

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

NAG.6: 3 residues within 4Å: Chain B: H.14, N.16, E.29 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.29 NAG.12: 3 residues within 4Å: Chain D: H.14, N.16, E.29 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parkash, V. et al., The Structure of the Glial Cell Line-Derived Neurotrophic Factor-Coreceptor Complex: Insights Into Ret Signaling and Heparin Binding. J.Biol.Chem. (2008)

Release Date

2008-10-21

Peptides

GDNF FAMILY RECEPTOR ALPHA-1: AC
GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

GDNF FAMILY RECEPTOR ALPHA-1

GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR