SMTL ID : 5u8r.1

Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-2-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 A: N.105, T.107, L.129, I.130, L.131, D.132, R.222, H.223 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: T.470, N.577, K.762 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 8 residues within 4Å: Chain D: N.105, T.107, L.129, I.130, L.131, D.132, R.222, H.223 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain D: T.470, N.577, K.762 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: W.79, K.80, L.81, N.84, R.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.79, A:L.81 Salt bridges: A:K.80, A:R.108 SO4.13: 5 residues within 4Å: Chain D: W.79, K.80, L.81, N.84, R.108 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.79, D:L.81 Salt bridges: D:K.80, D:R.108

4 x MLT: D-MALATE(Non-covalent)

MLT.4: 5 residues within 4Å: Chain A: Y.226, R.245, V.247, D.248 Chain B: D.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.248, A:D.248 Salt bridges: A:R.245 MLT.5: 2 residues within 4Å: Chain A: H.30, Y.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.54, A:Y.54 MLT.14: 5 residues within 4Å: Chain D: Y.226, R.245, V.247, D.248 Chain E: D.33 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.248, D:D.248 Salt bridges: D:R.245 MLT.15: 2 residues within 4Å: Chain D: H.30, Y.54 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.54, D:Y.54

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

NAG.6: 2 residues within 4Å: Chain A: E.20, N.21 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.504 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.504 NAG.8: 2 residues within 4Å: Chain A: N.610, H.758 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.610 NAG.9: 4 residues within 4Å: Chain A: Q.856, N.863, G.864, S.865 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.856 NAG.16: 2 residues within 4Å: Chain D: E.20, N.21 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain D: N.504 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.504 NAG.18: 2 residues within 4Å: Chain D: N.610, H.758 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.610 NAG.19: 4 residues within 4Å: Chain D: Q.856, N.863, G.864, S.865 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.856

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 5 residues within 4Å: Chain B: Q.41, S.42, H.43, S.46 Chain C: M.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.46 IMD.20: 5 residues within 4Å: Chain E: Q.41, S.42, H.43, S.46 Chain F: M.86 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., How ligand binds to the type 1 insulin-like growth factor receptor. Nat Commun (2018)

Release Date

2018-02-28

Peptides

Insulin-like growth factor 1 receptor: AD
Fv 24-60 heavy chain: BE
Fv 24-60 light chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
H

E
H

C
L

F
L

Insulin-like growth factor 1 receptor

Fv 24-60 heavy chain

Fv 24-60 light chain

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