SMTL ID : 4w4o.1

High-resolution crystal structure of Fc bound to its human receptor Fc-gamma-RI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-1-mer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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-GAL-MAN-NAG-FUC.1: 16 residues within 4Å: Chain A: F.18, F.20, P.21, P.22, K.23, E.35, T.37, V.41, D.42, Q.72, Y.73, N.74, T.76, R.78, K.111 Ligands: ACT.13 6 PLIP interactions: 6 interactions with chain A Water bridges: A:Y.73, A:D.26, A:E.35 Hydrogen bonds: A:F.20, A:K.23, A:K.23, A:E.35 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2: 17 residues within 4Å: Chain B: F.18, F.20, P.21, P.22, K.23, E.35, T.37, V.39, V.41, D.42, Q.72, N.74, T.76, R.78, K.111 Chain C: L.121, R.160 7 PLIP interactions: 7 interactions with chain B Water bridges: B:Y.73, B:D.26, B:E.35 Hydrogen bonds: B:F.20, B:K.23, B:E.35, B:E.35, B:T.37

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.3: 5 residues within 4Å: Chain C: L.43, N.44, E.62, D.63, S.65 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.62, C:E.62

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-MAN-MAN.4: 3 residues within 4Å: Chain C: N.144, S.146, H.147 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.87, H.212 Ligands: ACT.8, ACT.10 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.87, ACT.8, ACT.10 ZN.6: 2 residues within 4Å: Chain A: H.45, E.71 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.45, A:E.71, A:E.71 ZN.7: 3 residues within 4Å: Chain A: E.207, H.212 Ligands: ACT.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.212, H2O.1, H2O.7 ZN.15: 2 residues within 4Å: Chain B: E.122 Ligands: ACT.17 6 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.122, H2O.9, H2O.13, H2O.14, H2O.15, ACT.17 ZN.16: 2 residues within 4Å: Chain B: H.87, H.212 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.87, B:H.212 ZN.19: 1 residues within 4Å: Chain C: H.159 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.159, H2O.8, H2O.19, H2O.21, H2O.21

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 8 residues within 4Å: Chain A: H.87, Q.88, L.91, N.92, H.212 Ligands: ZN.5, ZN.7, ACT.10 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.87, A:H.212 ACT.9: 3 residues within 4Å: Chain A: H.45, P.48, Y.77 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.45, A:P.48 Hydrogen bonds: A:Y.77 ACT.10: 5 residues within 4Å: Chain A: H.87, N.211, H.212 Ligands: ZN.5, ACT.8 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.87, A:H.212 ACT.11: 5 residues within 4Å: Chain A: E.49, K.51, S.101, N.102, K.103 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.51 Water bridges: A:K.103 ACT.12: 2 residues within 4Å: Chain A: P.222, G.223 No protein-ligand interaction detected (PLIP) ACT.13: 3 residues within 4Å: Chain A: K.67, R.78 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.67 Salt bridges: A:R.78 ACT.17: 5 residues within 4Å: Chain B: E.122, L.209, H.210, Y.213 Ligands: ZN.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.209, B:H.210 Hydrogen bonds: B:H.210 ACT.20: 3 residues within 4Å: Chain C: H.159, R.160, Y.161 2 PLIP interactions: 2 interactions with chain C Water bridges: C:H.159 Salt bridges: C:H.159 ACT.21: 3 residues within 4Å: Chain C: A.181, V.183, T.184 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.184 Water bridges: C:A.181, C:S.185

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 7 residues within 4Å: Chain A: K.147, D.176, S.177, D.178 Chain B: N.167, K.186, T.188 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.147, A:D.176, B:N.167, B:N.167, B:K.186 Water bridges: B:T.188 GOL.18: 7 residues within 4Å: Chain A: N.167, K.186, T.188 Chain B: K.147, D.176, S.177, D.178 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.147, B:K.147, B:S.177, B:S.177, B:D.178, A:N.167, A:N.167, A:T.188 Water bridges: B:D.176, A:K.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiyoshi, M. et al., Structural basis for binding of human IgG1 to its high-affinity human receptor Fc gamma RI. Nat Commun (2015)

Release Date

2015-04-29

Peptides

Ig gamma-1 chain C region: AB
High affinity immunoglobulin gamma Fc receptor I: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ig gamma-1 chain C region

High affinity immunoglobulin gamma Fc receptor I