SMTL ID : 3n85.1

Crystallographic trimer of HER2 extracellular regions in complex with tryptophan-rich antibody fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- FUC: 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-FUC.1: 3 residues within 4Å: Chain A: Q.134, D.163, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.20: 3 residues within 4Å: Chain D: Q.134, D.163, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.39: 3 residues within 4Å: Chain G: Q.134, D.163, N.165 No protein-ligand interaction detected (PLIP)

3 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: 5 residues within 4Å: Chain A: C.230, C.233, N.237, S.239, G.240 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 5 residues within 4Å: Chain D: C.230, C.233, N.237, S.239, G.240 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 5 residues within 4Å: Chain G: C.230, C.233, N.237, S.239, G.240 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: T.45, V.69, R.70 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain D: T.45, V.69, R.70 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain G: T.45, V.69, R.70 Ligand excluded by PLIP

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

SO4.4: 5 residues within 4Å: Chain A: P.372, P.394, D.395, S.396 Chain C: W.100 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: H.456, H.473, T.474, A.475, N.476, R.477 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: Q.217, E.243, L.244 Chain G: K.128 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: A.15, Y.389, H.415, N.416, Q.424 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: R.514, R.523 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: V.575, A.576, R.577 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: K.148, N.154 Chain D: G.200 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: Q.462, R.495, H.497, V.507, N.508 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: V.408, R.410, R.437, E.438 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: E.485, G.486, G.502 Chain C: W.57, S.59 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain A: M.9, P.14, A.15, S.16, H.20, M.23, Y.419 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: H.152, K.153 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain A: A.15, S.16, E.18, H.447, H.448, T.474 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: S.30, S.31, R.66 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: P.59, S.60 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain A: E.373 Chain C: A.24, S.25, G.26, F.27, N.77 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain D: P.372, P.394, D.395, S.396 Chain F: W.100 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain D: H.456, H.473, T.474, A.475, N.476, R.477 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain A: K.128 Chain D: Q.217, E.243, L.244 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain D: A.15, Y.389, H.415, N.416, Q.424 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain D: R.514, R.523 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain D: V.575, A.576, R.577 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain D: K.148, N.154 Chain G: G.200 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain D: Q.462, R.495, H.497, V.507, N.508 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: V.408, R.410, R.437, E.438 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain D: E.485, G.486, G.502 Chain F: W.57, S.59 Ligand excluded by PLIP SO4.33: 7 residues within 4Å: Chain D: M.9, P.14, A.15, S.16, H.20, M.23, Y.419 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain D: H.152, K.153 Ligand excluded by PLIP SO4.35: 6 residues within 4Å: Chain D: A.15, S.16, E.18, H.447, H.448, T.474 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain E: S.30, S.31, R.66 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain E: P.59, S.60 Ligand excluded by PLIP SO4.38: 6 residues within 4Å: Chain D: E.373 Chain F: A.24, S.25, G.26, F.27, N.77 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain G: P.372, P.394, D.395, S.396 Chain I: W.100 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain G: H.456, H.473, T.474, A.475, N.476, R.477 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain D: K.128 Chain G: Q.217, E.243, L.244 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain G: A.15, Y.389, H.415, N.416, Q.424 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain G: R.514, R.523 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain G: V.575, A.576, R.577 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain A: G.200 Chain G: K.148, N.154 Ligand excluded by PLIP SO4.49: 5 residues within 4Å: Chain G: Q.462, R.495, H.497, V.507, N.508 Ligand excluded by PLIP SO4.50: 4 residues within 4Å: Chain G: V.408, R.410, R.437, E.438 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain G: E.485, G.486, G.502 Chain I: W.57, S.59 Ligand excluded by PLIP SO4.52: 7 residues within 4Å: Chain G: M.9, P.14, A.15, S.16, H.20, M.23, Y.419 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain G: H.152, K.153 Ligand excluded by PLIP SO4.54: 6 residues within 4Å: Chain G: A.15, S.16, E.18, H.447, H.448, T.474 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain H: S.30, S.31, R.66 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain H: P.59, S.60 Ligand excluded by PLIP SO4.57: 6 residues within 4Å: Chain G: E.373 Chain I: A.24, S.25, G.26, F.27, N.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fisher, R.D. et al., Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine. J.Mol.Biol. (2010)

Release Date

2010-07-28

Peptides

Receptor tyrosine-protein kinase erbB-2: ADG
Fab37 Light Chain: BEH
Fab37 Heavy Chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
L

E
L

H
L

C
H

F
H

I
H

Receptor tyrosine-protein kinase erbB-2

Fab37 Light Chain

Fab37 Heavy Chain

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