SMTL ID : 5k64.1

Crystal structure of VEGF binding IgG1-Fc (Fcab 448)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 13 residues within 4Å: Chain A: F.17, F.19, V.38, V.40, D.41, V.42, Q.71, N.73, T.75, Y.76, R.77 Ligands: NAG-NAG-BMA-MAN-NAG-MAN.2, NAG-NAG-BMA-MAN-NAG-MAN.2 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.2: 13 residues within 4Å: Chain B: F.17, F.19, K.22, T.36, V.38, V.40, D.41, Q.71, N.73, T.75, R.77 Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: L.170, N.171, Y.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.172, A:Y.172 GOL.5: 10 residues within 4Å: Chain B: P.23, S.151, D.152, I.153, A.154, T.174, T.175, P.176, P.177, L.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.153, B:T.175 GOL.6: 4 residues within 4Å: Chain B: L.170, N.171, Y.172, K.173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.172

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 7 residues within 4Å: Chain A: K.116, G.117, Q.118, R.120, Y.149, D.182, G.183 No protein-ligand interaction detected (PLIP)

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

2017-09-06

Peptides

Ig gamma-1 chain C region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ig gamma-1 chain C region