SMTL ID : 5ml9.1

Cocrystal structure of Fc gamma receptor IIIa interacting with Affimer F4, a specific binding protein which blocks IgG binding to the receptor.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: H.44, N.45, V.63, D.64, S.66, G.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.45, A:V.63, A:D.64 NAG.2: 4 residues within 4Å: Chain A: S.151, T.167, V.168, N.169 No protein-ligand interaction detected (PLIP) NAG.3: 6 residues within 4Å: Chain A: S.34, D.37, Q.41, Q.72, T.73, N.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.37, A:N.74, A:N.74

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

SO4.4: 5 residues within 4Å: Chain A: F.57, I.58, D.59, A.60, D.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.59, A:A.60, A:A.60 SO4.5: 7 residues within 4Å: Chain A: R.109, C.110, H.111, S.112, T.116, L.118, N.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.112, A:S.112, A:S.112, A:N.136 Salt bridges: A:H.111 SO4.11: 4 residues within 4Å: Chain A: K.143 Chain B: H.4, S.5, T.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.5, B:S.5, B:S.5 Salt bridges: B:H.4, A:K.143

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain A: L.124, G.127, K.128, G.129, Y.132, R.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.129, A:Y.132, A:R.155 PEG.7: 5 residues within 4Å: Chain A: T.145, K.147 Chain B: D.52, E.53, H.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.145, A:T.145 PEG.8: 5 residues within 4Å: Chain A: W.90, V.158, G.159, S.160, K.161 No protein-ligand interaction detected (PLIP) PEG.9: 8 residues within 4Å: Chain A: F.43, H.44, N.45, E.46, E.68, Y.69, R.70, P.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.43, A:E.46, A:E.46, A:E.68, A:R.70

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

CL.10: 3 residues within 4Å: Chain A: Q.15, H.107, Y.140 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, J.I. et al., Affimer proteins inhibit immune complex binding to Fc gamma RIIIa with high specificity through competitive and allosteric modes of action. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2017-12-13

Peptides

Low affinity immunoglobulin gamma Fc region receptor III-A: A
Affimer F4 with specificity for Fc gamma receptor IIIa: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Low affinity immunoglobulin gamma Fc region receptor III-A

Affimer F4 with specificity for Fc gamma receptor IIIa