SMTL ID : 5o4e.1

Crystal structure of VEGF in complex with heterodimeric Fcab JanusCT6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-2-1-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- MAN- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-NAG-FUC.1: 16 residues within 4Å: Chain A: F.17, F.19, K.22, T.36, V.38, V.40, D.41, Q.71, Y.72, N.73, T.75, R.77, K.110 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2, MPD.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.77, A:K.22, A:R.77 Water bridges: A:P.20, A:T.36, A:K.66 NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2: 15 residues within 4Å: Chain B: F.17, F.19, K.22, T.36, V.38, V.40, D.41, Q.71, Y.72, N.73, T.75, R.77, K.110 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.77 Water bridges: B:P.20, B:T.36

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

MAN-NAG.3: 5 residues within 4Å: Chain C: F.19, K.22, T.36, V.38 Ligands: MPD.9 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN.4: 11 residues within 4Å: Chain D: F.17, F.19, K.22, T.36, V.38, V.40, D.41, Q.71, N.73, T.75, R.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.36, D:T.36

10 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 8 residues within 4Å: Chain A: F.17, L.18, F.19, P.20, I.112 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.18 MPD.8: 5 residues within 4Å: Chain A: Q.138, N.166, T.187 Chain B: S.181, D.182 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.182 MPD.9: 11 residues within 4Å: Chain C: P.23, S.151, I.153, A.154, V.155, T.169, W.170, P.171, P.172, L.182 Ligands: MAN-NAG.3 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.153, C:T.169, C:L.182 MPD.10: 4 residues within 4Å: Chain D: G.169, L.170, N.171, Y.172 2 PLIP interactions: 2 interactions with chain D Water bridges: D:Y.172, D:K.173 MPD.11: 4 residues within 4Å: Chain D: N.215, Y.217, Q.219 Ligands: TRS.12 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.217 Water bridges: D:N.215 MPD.13: 5 residues within 4Å: Chain D: Y.137 Chain E: Q.10, Y.13, C.14, H.15 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.137, E:Q.10 MPD.14: 10 residues within 4Å: Chain E: E.18, P.41, L.42, M.43, I.64, M.66 Chain F: V.3, D.7, V.8, R.11 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:E.18, E:P.41, F:V.3 Hydrogen bonds: E:P.41 MPD.16: 8 residues within 4Å: Chain E: I.17, G.46, G.47 Chain F: L.20, V.21, D.22, Q.25, C.39 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:L.20 Hydrogen bonds: E:G.47 MPD.17: 9 residues within 4Å: Chain E: V.3, D.7, R.11 Chain F: E.18, P.41, L.42, M.43, I.64, Q.86 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:P.41, E:V.3 Hydrogen bonds: F:E.18 MPD.18: 5 residues within 4Å: Chain B: Y.137 Chain F: Q.10, Y.13, C.14, H.15 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Q.10 Water bridges: F:Y.13

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 10 residues within 4Å: Chain A: P.23, K.24, I.153, A.154, V.155, T.169, W.170, P.171, P.172, L.182 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.23, A:A.154 Hydrogen bonds: A:I.153 Water bridges: A:V.155, A:V.155

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.7: 7 residues within 4Å: Chain A: G.117, Q.118, R.120, Y.149, D.177, G.178, S.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.118, A:Q.118 CAC.15: 2 residues within 4Å: Chain E: R.70, H.78 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 5 residues within 4Å: Chain D: H.214, N.215, Y.217, T.218 Ligands: MPD.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.214, D:T.218 Water bridges: D:H.214, D:H.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lobner, E. et al., Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 angstrom crystal structure of the complex. MAbs (2017)

Release Date

2017-08-30

Peptides

Immunoglobulin gamma-1 heavy chain: A
Immunoglobulin gamma-1 heavy chain: BD
Immunoglobulin gamma-1 heavy chain: C
Vascular endothelial growth factor A: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

E
E

F
F

Immunoglobulin gamma-1 heavy chain

Immunoglobulin gamma-1 heavy chain

Immunoglobulin gamma-1 heavy chain

Vascular endothelial growth factor A