SMTL ID : 8vtp.1

Structure of FabS1CE-EPR-1, a high affinity antibody for the erythropoeitin receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-1-1-mer

Ligands

16 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 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: P.14, R.87, A.88, E.89 Ligand excluded by PLIP EDO.3: 9 residues within 4Å: Chain A: S.191, L.192, G.193, Q.195, Y.197, K.213, E.215, P.216 Ligands: NA.13 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: V.93, Q.109, G.110, T.111, L.112 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.38, E.46, S.63, E.89 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: P.41, T.91, L.112, T.114, E.151, Y.179 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: P.113, V.196, Q.198, T.201, V.203 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: Q.155, L.181, H.189 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain A: Q.39, Y.95 Chain B: Q.38, K.39, P.40, G.41, K.42 Ligands: NA.11 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: V.110, P.141 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: K.39, P.40, F.83, A.84 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: A.111, A.112 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: S.156, G.157, N.158, S.159 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: R.142, A.144, E.161, L.175 Ligands: EDO.27 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: E.161, S.162, V.163 Ligands: EDO.24 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: K.145, E.195, T.197, S.202 Ligand excluded by PLIP

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

ACT.4: 6 residues within 4Å: Chain A: S.123, V.124, F.125, V.210, K.212 Chain B: E.123 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.125 Hydrogen bonds: A:P.122, A:V.124 Water bridges: A:K.212 Salt bridges: A:K.212 ACT.16: 5 residues within 4Å: Chain B: T.197, G.199, T.200, T.201, S.202 No protein-ligand interaction detected (PLIP) ACT.19: 4 residues within 4Å: Chain A: Y.101 Chain B: Y.49, Y.55, S.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.56 Water bridges: B:L.54, B:S.56 ACT.25: 8 residues within 4Å: Chain A: K.217 Chain B: P.119, Y.186, F.207, N.208, R.209, G.210, E.211 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.217 Hydrophobic interactions: B:P.119 Hydrogen bonds: B:G.210 Water bridges: B:Y.186

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

CL.8: 2 residues within 4Å: Chain A: Y.57, T.58 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: A.161, L.162, T.163, S.164 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain B: Q.155, S.156 Ligand excluded by PLIP

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

NA.10: 4 residues within 4Å: Chain A: P.126, L.127, A.128 Chain B: P.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.126, A:A.128 NA.11: 4 residues within 4Å: Chain A: Q.39, V.93, Y.95 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.95 Water bridges: A:Q.39, A:Y.95 NA.12: 1 residues within 4Å: Chain A: V.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.153 NA.13: 3 residues within 4Å: Chain A: T.196, K.213 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.196, A:K.213 NA.30: 2 residues within 4Å: Chain B: S.9, G.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.9

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

NH4.14: 4 residues within 4Å: Chain B: K.188, H.189, K.190, R.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.209 Water bridges: B:K.188, B:K.190

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

PEG.26: 7 residues within 4Å: Chain B: P.141, E.143, A.144, K.145, T.197, Q.198, G.199 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.143, B:Q.198, B:G.199

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

S1CE VARIANT OF FAB-EPR-1 heavy chain

S1CE VARIANT OF FAB-EPR-1 light chain

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