SMTL ID : 8acf.1

Structure of the argX-117 in complex with a complement C2 fragment at low pH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 5 residues within 4Å: Chain A: G.90, G.91, N.92, Q.110 Chain D: Y.34 No protein-ligand interaction detected (PLIP)

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 5 residues within 4Å: Chain A: R.104, G.105, S.106, G.119, E.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.105, A:S.106, A:E.120, A:E.120 EPE.5: 9 residues within 4Å: Chain D: L.15, A.84, I.110, R.112, T.113, S.172, K.173, D.174, S.175 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.113 Water bridges: D:S.175 Salt bridges: D:R.112

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: R.83, L.84 Chain B: N.33, E.99, D.103 Chain D: Y.100 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:Y.100, A:R.83, B:E.99, B:D.103, H2O.3, H2O.5

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

CL.4: 4 residues within 4Å: Chain C: S.54, G.55, D.56, G.57 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain D: P.63, D.64, R.65 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olesen, H.G. et al., Structure-function analysis of ARGX-117, a calcium- and pH-dependent clinical phase complement C2 blocking antibody. To be published

Release Date

2024-01-17

Peptides

Complement C2b fragment: A
Heavy chain of mAb ARGX-117 Fab: B
Nanobody specific for the kappa-light chain: C
Light chain of mAb ARGX-117 Fab: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
K

D
L

Complement C2b fragment

Heavy chain of mAb ARGX-117 Fab

Nanobody specific for the kappa-light chain

Light chain of mAb ARGX-117 Fab

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