SMTL ID : 8os6.1

Structure of a GFRA1/GDNF LICAM complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

hetero-10-10-mer

Ligands

4 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: 8 residues within 4Å: Chain C: N.248, Q.251, A.252, N.255 Chain E: S.226, G.227, N.228, S.229 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain J: H.12, L.13, N.14, D.17, E.27 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain N: H.12, L.13, N.14, E.27 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain P: H.12, L.13, N.14, D.17, E.27 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.2: 5 residues within 4Å: Chain D: H.12, L.13, N.14, K.25, E.27 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.3: 4 residues within 4Å: Chain F: H.12, L.13, N.14, E.27 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.4: 5 residues within 4Å: Chain H: H.12, L.13, N.14, D.17, E.27 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.7: 9 residues within 4Å: Chain I: S.225, S.226, G.227, N.228, S.229 Chain O: N.248, Q.251, A.252, N.255 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain O Hydrogen bonds: I:N.228, I:S.229, O:N.255, I:S.226 Hydrophobic interactions: O:A.252

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

NAG.9: 4 residues within 4Å: Chain B: H.12, L.13, N.14, E.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.14, B:E.27 NAG.10: 4 residues within 4Å: Chain E: N.255, G.258, S.259 Chain K: N.228 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain K Hydrophobic interactions: E:N.255 Hydrogen bonds: K:N.228 NAG.11: 8 residues within 4Å: Chain A: S.226, G.227, N.228, S.229 Chain G: N.248, Q.251, A.252, N.255 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.228 NAG.12: 5 residues within 4Å: Chain I: Q.251, N.255 Chain S: S.226, G.227, N.228 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain S Hydrogen bonds: I:N.255 Hydrophobic interactions: S:N.228 NAG.13: 7 residues within 4Å: Chain G: G.227, N.228, S.229 Chain K: N.248, Q.251, A.252, N.255 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.228 NAG.14: 4 residues within 4Å: Chain L: H.12, L.13, N.14, D.17 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:H.12 Hydrogen bonds: L:N.14 NAG.15: 5 residues within 4Å: Chain M: Q.251, A.252, N.255 Chain Q: G.227, N.228 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.228 NAG.16: 4 residues within 4Å: Chain R: H.12, L.13, N.14, D.17 No protein-ligand interaction detected (PLIP) NAG.17: 6 residues within 4Å: Chain M: S.225, S.226, N.228 Chain S: Q.251, A.252, N.255 6 PLIP interactions: 4 interactions with chain M, 2 interactions with chain S Hydrophobic interactions: M:N.228, S:N.255 Hydrogen bonds: M:S.226, M:S.226, M:N.228, S:N.255 NAG.18: 3 residues within 4Å: Chain T: H.12, L.13, N.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Houghton, F.M. et al., Architecture and regulation of a GDNF-GFR alpha 1 synaptic adhesion assembly. Nat Commun (2023)

Release Date

2023-11-29

Peptides

GDNF family receptor alpha: ACEGIKMOQS
Glial cell line-derived neurotrophic factor: BDFHJLNPRT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

Q
Q

S
S

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

T
T

GDNF family receptor alpha

Glial cell line-derived neurotrophic factor