SMTL ID : 6yax.1

Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain F: N.145, H.146, S.147, H.148 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 13 residues within 4Å: Chain A: H.35, E.99, D.102, A.103, F.104 Chain C: P.117, N.157, G.159, Y.160 Chain D: Y.33, H.36, W.93, V.101 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.159 Water bridges: C:K.116, C:Y.160, D:H.36 PG4.5: 12 residues within 4Å: Chain B: Y.33, H.36, W.93, V.101 Chain E: H.35, Y.59, E.99, D.102, A.103, F.104 Chain F: G.159, Y.160 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Water bridges: F:K.116, F:G.159 Hydrogen bonds: E:D.102

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

NAG.3: 4 residues within 4Å: Chain C: N.145, H.146, S.147, H.148 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.145, C:S.147, C:S.147

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: G.42, K.43, G.44 Chain D: P.8, D.87, Y.89, G.105, G.106, T.107, K.108 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:G.42, D:D.87, D:Y.89, D:G.106, D:K.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fisher, H. et al., Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05). To Be Published

Release Date

2021-10-06

Peptides

5C05 F(ab) heavy chain: AE
5C05 F(ab) light chain: BD
Low affinity immunoglobulin gamma Fc region receptor II-c: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
HHH

E
III

B
MMM

D
LLL

C
AAA

F
BBB

5C05 F(ab) heavy chain

5C05 F(ab) light chain

Low affinity immunoglobulin gamma Fc region receptor II-c