SMTL ID : 8vui.1

Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: L.144, V.172, S.180, L.181, S.182 Chain B: T.178 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:S.176, B:S.176, B:T.178, B:T.178, A:S.182 Hydrogen bonds: A:S.182 EDO.6: 5 residues within 4Å: Chain B: T.197, G.199, T.200, T.201, S.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.199 EDO.7: 7 residues within 4Å: Chain B: Q.37, L.47, P.59, R.61, F.62, E.81, D.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.37, B:E.81, B:D.82 Water bridges: B:K.39

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

NA.2: 4 residues within 4Å: Chain A: V.5, E.6, S.7, S.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.5, A:A.23 NA.3: 3 residues within 4Å: Chain A: L.192, Q.195, Y.197 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.213, A:K.213 NA.8: 6 residues within 4Å: Chain A: H.167 Chain B: T.164, E.165, D.167, T.172, S.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.164, B:S.174 NA.9: 5 residues within 4Å: Chain B: V.110, A.111, A.112, Y.140, Q.198 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.111, B:A.111

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

CL.4: 2 residues within 4Å: Chain A: S.123, V.124 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: T.196, K.213 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: Q.166, D.167, S.168 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: I.113, H.114 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: L.121, D.122, P.145, T.148 Ligand excluded by PLIP

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

NAG.11: 3 residues within 4Å: Chain C: G.47, V.48, N.52 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.48 Hydrogen bonds: C:G.47, C:N.52

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

CIT.12: 7 residues within 4Å: Chain C: E.24, E.25, L.26, Y.109, H.110, R.111 Ligands: NH4.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.25, C:L.26, C:H.110

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.13: 2 residues within 4Å: Chain C: R.108 Ligands: CIT.12 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.99

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

S1CE VARIANT OF FAB-EPR-1 heavy chain: A
S1CE VARIANT OF FAB-EPR-1 light chain: B
Erythropoietin receptor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

C
D

S1CE VARIANT OF FAB-EPR-1 heavy chain

S1CE VARIANT OF FAB-EPR-1 light chain

Erythropoietin receptor

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