SMTL ID : 5zmj.1

Crystal structure of the Fab region of a neutralizing fully human antibody against GM-CSF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.86, K.106 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.84 Salt bridges: A:R.86, A:K.106 SO4.4: 3 residues within 4Å: Chain B: V.178, K.179, A.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.179, B:A.180 SO4.5: 4 residues within 4Å: Chain B: T.127, Y.163, K.189, Y.195 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.163, B:Y.195 Water bridges: B:V.128, B:K.189, B:K.189, B:Y.195, B:Y.195 Salt bridges: B:K.189 SO4.6: 2 residues within 4Å: Chain B: A.180, G.181 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.181 Water bridges: B:V.182, B:V.182, A:S.205 SO4.7: 3 residues within 4Å: Chain A: H.197 Chain B: Q.190, S.191 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Water bridges: A:V.196, A:T.198, A:T.198, B:S.191, B:N.192 Salt bridges: A:H.197 Hydrogen bonds: B:S.191, B:S.191 SO4.8: 2 residues within 4Å: Chain B: R.74, S.83 5 PLIP interactions: 5 interactions with chain B Water bridges: B:N.72, B:N.72, B:R.74, B:R.74 Salt bridges: B:R.74

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: W.66, R.118 Chain B: R.118 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.118, B:R.118, A:R.118 NA.3: 3 residues within 4Å: Chain A: L.91, D.92, T.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.93, A:T.93 NA.9: 2 residues within 4Å: Chain B: T.185, T.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.186, B:T.186 NA.10: 3 residues within 4Å: Chain A: R.121, F.122 Chain B: Y.52 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.52, A:F.122 Water bridges: B:Y.52, B:Y.54, B:R.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Angkawidjaja, C. et al., Crystal structure of the Fab region of a neutralizing antibody against granulocyte-macrophage colony-stimulating factor. Acta Crystallogr.,Sect.F (2019)

Release Date

2019-04-17

Peptides

Heavy chain of a Fab fraction of human IgG: A
Light chain of a Fab fraction of human IgG: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Heavy chain of a Fab fraction of human IgG

Light chain of a Fab fraction of human IgG