SMTL ID : 5c6w.1

anti-CXCL13 scFv - E10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: G.201, V.202, S.203 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: K.23, A.24 Ligands: EDO.8 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: S.7, G.8 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: H.204 Ligands: EDO.7 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: K.12, K.13, S.16 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain B: N.196 Ligand excluded by PLIP

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: G.27, T.28, F.29, Y.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.28, A:F.29, A:Y.32 SO4.6: 4 residues within 4Å: Chain A: N.196, N.197, R.198, H.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.197, A:R.198 Salt bridges: A:R.198, A:H.204 SO4.27: 3 residues within 4Å: Chain B: N.197, R.198, H.204 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.197, B:R.198 Water bridges: B:N.196, B:R.198, B:H.204 Salt bridges: B:R.198, B:H.204 SO4.28: 3 residues within 4Å: Chain B: Q.1, V.2, R.98 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.2 Water bridges: B:R.98, B:R.98, B:D.115, B:D.115 Salt bridges: B:R.98 SO4.29: 1 residues within 4Å: Chain B: K.19 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.19

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

EDO.7: 3 residues within 4Å: Chain A: R.198, S.207 Ligands: CL.4 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: S.25, G.26 Ligands: CL.2 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: Y.174, D.175 Ligands: EDO.17 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: P.100, I.111, F.193, P.199 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: S.203, R.205, Q.223, E.225 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.210, S.211, G.212 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: G.42, Q.43, G.44, Y.231, T.245 Chain B: G.42, Q.43, G.44, T.245 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: Q.181, K.189, L.191, G.201, V.202, F.206 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: N.59, A.235, T.236, D.239, T.240, Y.241 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: A.24, S.30, S.31, Y.32, P.53, D.73, S.77, T.78 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: P.110, D.112, D.175, W.176 Ligands: EDO.9 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: Y.102, D.104, S.106, Y.109 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: S.144, A.145 Chain B: K.248 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: P.14, S.126, S.127 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: A.9, E.10, V.11 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: T.167, S.168, N.213 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: L.45, E.46, W.47, A.145, Y.241, V.242, F.243 Ligand excluded by PLIP EDO.30: 2 residues within 4Å: Chain B: S.7, G.8 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: S.7, K.19, S.21, Y.80 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain B: Q.181, K.189, L.191, G.201, V.202, S.203, F.206 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain B: A.24, S.31, Y.32, I.34, P.53, S.77 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: F.55, Y.103, Y.108 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain B: S.16, S.17 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain A: K.186 Chain B: R.87, S.88 Ligand excluded by PLIP EDO.37: 2 residues within 4Å: Chain B: S.200, G.201 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: P.100, I.111, D.115, F.193, P.199 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain B: S.203, R.205, Q.223 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain B: N.59, D.112, A.235, D.239, T.240, Y.241 Ligand excluded by PLIP EDO.41: 2 residues within 4Å: Chain B: S.126, S.127 Ligand excluded by PLIP

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

PEG.24: 3 residues within 4Å: Chain A: P.149, S.163 Ligands: PEG.42 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.163, A:T.165, A:T.165 PEG.42: 4 residues within 4Å: Chain B: S.151, V.152, S.153 Ligands: PEG.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.153 Water bridges: B:S.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tu, C. et al., Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair. To Be Published

Release Date

2015-11-04

Peptides

Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
J

Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84