SMTL ID : 8vu4.1

Structure of FabS1CE4-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: V.155, S.156, W.157, G.160, L.162, T.163, V.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.157, A:W.157, A:G.160 EDO.2: 4 residues within 4Å: Chain A: N.202, H.203, N.207, T.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.202, A:T.208 EDO.22: 7 residues within 4Å: Chain C: K.43, G.44 Chain D: S.9, T.85, Y.87, Q.100, G.101 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.43, D:S.9 EDO.23: 6 residues within 4Å: Chain D: P.119, F.207, N.208, R.209, G.210, E.211 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.210, D:E.211, D:E.211

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

CL.3: 3 residues within 4Å: Chain A: T.194, Q.195, T.196 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: Q.155, S.156, N.158 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: Q.39 Chain B: Q.38, G.41 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: P.113, V.203 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: Q.155 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: A.111, A.112 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: D.211 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: P.113, V.196, Q.198 Ligand excluded by PLIP

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

NA.4: 2 residues within 4Å: Chain A: S.135, G.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.138 NA.5: 3 residues within 4Å: Chain A: E.151, P.152, V.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.151, A:V.153 NA.6: 5 residues within 4Å: Chain A: Y.95, Q.109 Chain B: G.41, K.42, A.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.95 NA.12: 5 residues within 4Å: Chain B: M.4, T.5, Q.6, G.99, Q.100 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.6, B:Q.100, B:Q.100, D:K.188, D:K.188 NA.13: 1 residues within 4Å: Chain B: S.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.200 NA.14: 5 residues within 4Å: Chain B: N.158, S.159, Q.160, T.178, T.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.158, B:Q.160, B:T.180 NA.15: 2 residues within 4Å: Chain B: Y.149, N.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.152 NA.17: 4 residues within 4Å: Chain C: A.88, T.91, V.115, S.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.115 Water bridges: C:N.117 NA.18: 6 residues within 4Å: Chain B: S.162 Chain C: P.170, V.172, S.180, L.181, S.182 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:V.172, C:S.180, C:S.182, B:S.162 NA.19: 6 residues within 4Å: Chain C: P.152, V.153, N.202, H.203, K.204, P.205 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.202, C:K.204 NA.20: 1 residues within 4Å: Chain C: E.151 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.151 NA.25: 1 residues within 4Å: Chain D: Q.155 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.155, D:Q.155 NA.26: 2 residues within 4Å: Chain D: T.204, S.206 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.206 NA.27: 3 residues within 4Å: Chain D: S.14, V.15, K.107 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.15

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

PEG.21: 6 residues within 4Å: Chain D: G.157, N.158, S.159, Q.160, T.178, T.180 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.159, D:T.180 Water bridges: D:T.180

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

S1CE4 VARIANT OF FAB-EPR-1 heavy chain: AC
S1CE4 VARIANT OF FAB-EPR-1 light chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
A

B
C

D
G

S1CE4 VARIANT OF FAB-EPR-1 heavy chain

S1CE4 VARIANT OF FAB-EPR-1 light chain

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