SMTL ID : 5u8q.1

Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor in complex with IGF-I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.27 Å

Oligo State

hetero-2-2-2-2-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: 6 residues within 4Å: Chain A: N.105, L.129, I.130, L.131, D.132, R.222 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: Q.856, N.863, G.864, S.865, W.866 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain E: N.105, L.129, I.130, L.131, D.132, R.222 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain E: Q.856, N.863, G.864, S.865, W.866 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.2: 2 residues within 4Å: Chain A: T.470, N.577 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.11: 2 residues within 4Å: Chain E: T.470, N.577 No protein-ligand interaction detected (PLIP)

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

SO4.4: 4 residues within 4Å: Chain A: K.80, L.81, N.84, R.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.81, A:L.81 Salt bridges: A:R.108 SO4.5: 1 residues within 4Å: Chain A: R.793 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.793 SO4.13: 4 residues within 4Å: Chain E: K.80, L.81, N.84, R.108 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.81, E:L.81 Salt bridges: E:R.108 SO4.14: 1 residues within 4Å: Chain E: R.793 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.793

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

MLT.6: 4 residues within 4Å: Chain A: Y.226, R.245, D.248 Chain C: D.33 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.248, A:D.248, A:D.248, C:D.33 Salt bridges: A:R.245 MLT.15: 4 residues within 4Å: Chain E: Y.226, R.245, D.248 Chain G: D.33 5 PLIP interactions: 1 interactions with chain G, 4 interactions with chain E Hydrogen bonds: G:D.33, E:D.248, E:D.248, E:D.248 Salt bridges: E:R.245

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

NAG.7: 3 residues within 4Å: Chain A: E.20, N.21 Chain C: S.77 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.77 NAG.8: 1 residues within 4Å: Chain A: N.504 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.504 NAG.9: 1 residues within 4Å: Chain A: N.850 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain E: E.20, N.21 Chain G: S.77 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.77 NAG.17: 1 residues within 4Å: Chain E: N.504 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.504 NAG.18: 1 residues within 4Å: Chain E: N.850 No protein-ligand interaction detected (PLIP)

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: AE
Insulin-like growth factor I: BF
Fv 24-60 heavy chain: CG
Fv 24-60 light chain: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

B
B

F
B

C
H

G
H

D
L

H
L

Insulin-like growth factor 1 receptor

Insulin-like growth factor I

Fv 24-60 heavy chain

Fv 24-60 light chain

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