SMTL ID : 8ts5.1 (1 other biounit)

Structure of the apo FabS1C_C1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-1-mer

Ligands

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.1: 8 residues within 4Å: Chain A: Y.147, E.150, P.151, V.152, F.168, P.169, A.170, L.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.147, A:E.150, A:V.152, A:A.170 BTB.19: 7 residues within 4Å: Chain A: T.133, S.134 Chain B: P.116, S.117, V.118, V.206, K.208 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.208, B:K.208, A:S.134

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

PEG.2: 6 residues within 4Å: Chain A: P.41, E.150, A.170, Y.178 Ligands: PEG.7, PEG.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.150 Water bridges: A:L.172 PEG.3: 4 residues within 4Å: Chain A: E.6, S.7, Q.107 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) PEG.4: 6 residues within 4Å: Chain A: A.127, K.216 Chain B: F.121, P.122, E.214 Ligands: CL.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.127 PEG.7: 4 residues within 4Å: Chain A: L.110, P.151 Ligands: PEG.2, EDO.6 No protein-ligand interaction detected (PLIP) PEG.18: 5 residues within 4Å: Chain B: T.200, G.202, T.203, T.204, S.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.202 PEG.20: 5 residues within 4Å: Chain B: L.157, Q.158, S.159, G.160, N.161 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.157, B:S.159, B:G.160 PEG.21: 4 residues within 4Å: Chain B: K.148, S.150, Y.152, E.198 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.148, B:S.150, B:S.150 PEG.25: 5 residues within 4Å: Chain A: A.170, V.171 Chain B: E.164, S.165 Ligands: PEG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.170 Water bridges: A:L.172 PEG.30: 3 residues within 4Å: Chain B: A.115, T.204, V.206 4 PLIP interactions: 4 interactions with chain B Water bridges: B:A.114, B:Q.201, B:Q.201, B:Q.201 PEG.31: 4 residues within 4Å: Chain C: Y.55, G.56, Y.57, T.58 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.58, C:T.58

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

EDO.5: 1 residues within 4Å: Chain A: K.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.212 EDO.6: 6 residues within 4Å: Chain A: G.9, G.10, T.109, L.110 Ligands: PEG.3, PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.109, A:L.110 EDO.8: 6 residues within 4Å: Chain A: G.66, R.67, F.68, T.69, Q.82, N.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.68, A:T.69, A:N.84 EDO.9: 3 residues within 4Å: Chain A: R.87, A.88, E.89 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.87, A:R.87, A:E.89, A:E.89 Water bridges: A:A.88 EDO.10: 4 residues within 4Å: Chain A: L.11, T.118, P.149, P.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.118 Water bridges: A:L.11 EDO.22: 6 residues within 4Å: Chain B: V.149, S.150, W.151, L.157, Q.158, S.162 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.151, B:W.151, B:S.162, B:S.162 Water bridges: B:V.149, B:S.180 EDO.23: 8 residues within 4Å: Chain B: Q.37, K.39, K.45, P.59, R.61, F.62, E.81, D.82 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.37, B:Q.37, B:K.39, B:K.45, B:R.61 EDO.24: 4 residues within 4Å: Chain B: Y.152, N.155, E.198, T.207 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.155, B:T.207, B:T.207 EDO.26: 4 residues within 4Å: Chain B: E.146, Q.201, G.202 Ligands: NA.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.146, B:G.202

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

ACT.11: 3 residues within 4Å: Chain A: N.157, S.158, A.160 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.160 ACT.12: 4 residues within 4Å: Chain A: Y.100 Chain B: Y.91, Y.92 Chain C: Y.54 No protein-ligand interaction detected (PLIP) ACT.32: 2 residues within 4Å: Chain C: T.118, S.205 No protein-ligand interaction detected (PLIP) ACT.33: 4 residues within 4Å: Chain C: I.51, G.56, S.71, A.72 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.72, C:A.72

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

NA.13: 4 residues within 4Å: Chain A: V.171, S.179 Chain B: T.181 Ligands: NA.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.181, B:T.181 Water bridges: A:S.179 NA.14: 4 residues within 4Å: Chain A: T.153, V.154, S.155, N.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.153, A:S.155, A:N.201 NA.15: 8 residues within 4Å: Chain A: F.168, P.169, A.170, S.179, L.180, S.181 Chain B: S.165 Ligands: NA.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.165, B:S.165, A:S.181 NA.16: 1 residues within 4Å: Chain A: E.89 No protein-ligand interaction detected (PLIP) NA.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.28: 3 residues within 4Å: Chain B: P.144, E.146 Ligands: EDO.26 No protein-ligand interaction detected (PLIP) NA.34: 4 residues within 4Å: Chain C: I.29, S.32, S.52, A.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.29 NA.35: 3 residues within 4Å: Chain C: E.150, P.151, V.152 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.152, C:V.152

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

CL.17: 4 residues within 4Å: Chain A: A.127, S.129 Chain B: F.121 Ligands: PEG.4 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: Q.127, S.130, G.131, T.132 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruce, H.A. et al., Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Protein Sci. (2024)

Release Date

2023-11-22

Peptides

S1C variant of Fab C1 heavy chain: AC
S1C variant of Fab C1 light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
G

S1C variant of Fab C1 heavy chain

S1C variant of Fab C1 light chain

Related Entries With Identical Sequence