SMTL ID : 7ab8.1

Crystal structure of a GDNF-GFRalpha1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain B: H.11, L.12, N.13, D.16, E.26 Chain D: K.55 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain B: K.55 Chain D: H.11, L.12, N.13, D.16, E.26 No protein-ligand interaction detected (PLIP)

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

EDO.2: 2 residues within 4Å: Chain A: P.125, L.126 No protein-ligand interaction detected (PLIP) EDO.3: 8 residues within 4Å: Chain A: K.40, R.41, H.44, K.45, R.48, G.148, T.149, V.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:R.48, A:R.48 EDO.4: 7 residues within 4Å: Chain A: C.28, T.29, V.37, C.38, V.84, A.86, C.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.28 Water bridges: A:T.29 EDO.5: 6 residues within 4Å: Chain A: L.98, Q.101, E.178, R.181, F.182 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.101, A:Q.101 EDO.6: 4 residues within 4Å: Chain A: S.103, T.106, N.107, V.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.106 EDO.13: 2 residues within 4Å: Chain C: P.125, L.126 No protein-ligand interaction detected (PLIP) EDO.14: 8 residues within 4Å: Chain C: K.40, R.41, H.44, K.45, R.48, G.148, T.149, V.150 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.41, C:R.48, C:R.48 EDO.15: 7 residues within 4Å: Chain C: C.28, T.29, V.37, C.38, V.84, A.86, C.87 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.28 Water bridges: C:T.29 EDO.16: 6 residues within 4Å: Chain C: L.98, Q.101, E.178, R.181, F.182 Ligands: PEG.18 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.101, C:Q.101 EDO.17: 4 residues within 4Å: Chain C: S.103, T.106, N.107, V.150 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.106

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

PEG.7: 8 residues within 4Å: Chain A: Q.101, K.105, R.111, L.114, A.115, F.118, F.182 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.101, A:K.105, A:A.115 PEG.8: 8 residues within 4Å: Chain A: E.124, P.125, S.127, L.128, G.130, A.190, N.194 Ligands: PEG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.125, A:N.194 PEG.9: 11 residues within 4Å: Chain A: K.40, H.44, S.88, Y.89, D.91, P.95, L.100, T.149, V.150, T.152, F.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.40, A:Y.89 PEG.10: 11 residues within 4Å: Chain A: L.47, R.48, F.51, D.52, R.113, L.141, S.144, G.145, L.146, I.147, G.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.113, A:L.141, A:S.144, A:I.147, A:I.147 PEG.11: 8 residues within 4Å: Chain A: P.123, P.125, D.188, N.189, A.190, C.191, R.193 Ligands: PEG.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.190, A:R.193, A:R.193 Water bridges: A:E.124, A:E.124 PEG.18: 8 residues within 4Å: Chain C: Q.101, K.105, R.111, L.114, A.115, F.118, F.182 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.101, C:K.105, C:A.115 PEG.19: 8 residues within 4Å: Chain C: E.124, P.125, S.127, L.128, G.130, A.190, N.194 Ligands: PEG.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.125, C:N.194 PEG.20: 11 residues within 4Å: Chain C: K.40, H.44, S.88, Y.89, D.91, P.95, L.100, T.149, V.150, T.152, F.166 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.40, C:Y.89 PEG.21: 11 residues within 4Å: Chain C: L.47, R.48, F.51, D.52, R.113, L.141, S.144, G.145, L.146, I.147, G.148 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.113, C:L.141, C:S.144, C:I.147, C:I.147 PEG.22: 8 residues within 4Å: Chain C: P.123, P.125, D.188, N.189, A.190, C.191, R.193 Ligands: PEG.19 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.190, C:R.193, C:R.193 Water bridges: C:E.124, C:E.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, S.E. et al., A two-site flexible clamp mechanism for RET-GDNF-GFR alpha 1 assembly reveals both conformational adaptation and strict geometric spacing. Structure (2021)

Release Date

2021-01-13

Peptides

GDNF family receptor alpha: 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

Glial cell line-derived neurotrophic factor