SMTL ID : 4zxb.1

Structure of the human insulin receptor ectodomain, IRDeltabeta construct, in complex with four Fab molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-2-2-2-2-2-mer

Ligands

6 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.1: 5 residues within 4Å: Chain E: E.6, H.21, E.22, E.24, N.25 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.3: 6 residues within 4Å: Chain A: D.54, N.56 Chain E: R.252, N.255, S.257, F.258 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.258 NAG-NAG-FUC.6: 4 residues within 4Å: Chain E: N.606, K.614, V.746, S.748 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.746 NAG-NAG-FUC.11: 5 residues within 4Å: Chain J: E.6, H.21, E.22, E.24, N.25 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.13: 6 residues within 4Å: Chain F: D.54, N.56 Chain J: R.252, N.255, S.257, F.258 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:F.258 NAG-NAG-FUC.16: 4 residues within 4Å: Chain J: N.606, K.614, V.746, S.748 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:V.746

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

NAG-NAG-BMA.2: 10 residues within 4Å: Chain E: N.111, T.113, S.134, R.135, I.136, L.137, D.138, S.198, L.213, R.229 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.138 NAG-NAG-BMA.12: 10 residues within 4Å: Chain J: N.111, T.113, S.134, R.135, I.136, L.137, D.138, S.198, L.213, R.229 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:D.138

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

NAG-NAG-BMA-MAN-NAG-FUC.4: 1 residues within 4Å: Chain E: N.397 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-FUC.14: 1 residues within 4Å: Chain J: N.397 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.5: 3 residues within 4Å: Chain E: L.387, N.418, T.420 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.387 Hydrogen bonds: E:N.418, E:T.420 NAG-FUC.7: 4 residues within 4Å: Chain E: Y.829, N.858, Y.879, Y.881 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.829, E:Y.881 NAG-FUC.15: 3 residues within 4Å: Chain J: L.387, N.418, T.420 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:L.387 Hydrogen bonds: J:N.418 NAG-FUC.17: 4 residues within 4Å: Chain J: Y.829, N.858, Y.879, Y.881 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:Y.829, J:Y.881

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

NAG.8: 2 residues within 4Å: Chain E: N.16, T.18 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.18 Hydrogen bonds: E:N.16 NAG.9: 4 residues within 4Å: Chain E: N.108, M.110, K.190, N.215 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.190 Hydrogen bonds: E:N.215 NAG.10: 2 residues within 4Å: Chain E: Y.512, N.514 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain J: N.16, T.18 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:T.18 Hydrogen bonds: J:N.16 NAG.19: 4 residues within 4Å: Chain J: N.108, M.110, K.190, N.215 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:K.190 Hydrogen bonds: J:N.215 NAG.20: 2 residues within 4Å: Chain J: Y.512, N.514 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Croll, T.I. et al., Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain. Structure (2016)

Release Date

2016-02-24

Peptides

Fab 83-7 heavy chain: AF
Fab 83-7 light chain: BG
Fab 83-14 heavy chain: CH
Fab 83-14 light chain: DI
Insulin receptor: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

B
B

G
B

C
C

H
C

D
D

I
D

E
E

J
E

Fab 83-7 heavy chain

Fab 83-7 light chain

Fab 83-14 heavy chain

Fab 83-14 light chain

Insulin receptor

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