SMTL ID : 8vtr.1

Structure of FabS1CE3-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor (orthorhombic form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: Y.55, S.56, Y.57, T.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.55, A:T.58 PEG.4: 5 residues within 4Å: Chain B: K.145, S.147, Y.149, E.195, T.197 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.145, B:S.147, B:T.197

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: V.2, Y.32, R.98, Y.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.98, A:R.98 Water bridges: A:D.105 EDO.3: 2 residues within 4Å: Chain B: T.200, S.202 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain B: K.107, R.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.108 EDO.6: 2 residues within 4Å: Chain B: S.182, D.185 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.182 EDO.7: 6 residues within 4Å: Chain B: P.119, F.207, N.208, R.209, G.210, E.211 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.210, B:E.211, B:E.211 Water bridges: B:Y.186, B:Y.186, B:N.208

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.8: 3 residues within 4Å: Chain B: S.121, D.122, E.123 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.122 Hydrogen bonds: B:D.122, B:D.122, B:E.123 Water bridges: B:P.120

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

CL.9: 1 residues within 4Å: Chain B: R.142 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: R.209 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruce, H.A. et al., Antigen-binding fragments with improved crystal lattice packing and enhanced conformational flexibility at the elbow region as crystallization chaperones. Protein Sci. (2024)

Release Date

2024-07-10

Peptides

S1CE3 VARIANT OF FAB-EPR-1 heavy chain: A
S1CE3 VARIANT OF FAB-EPR-1 light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

S1CE3 VARIANT OF FAB-EPR-1 heavy chain

S1CE3 VARIANT OF FAB-EPR-1 light chain

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