SMTL ID : 6ol5.1

Structure of iglb12 Fab in complex with anti-idiotype ib3 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NH4.1: 2 residues within 4Å: Chain A: T.87, E.89 Ligand excluded by PLIP NH4.2: 6 residues within 4Å: Chain A: Y.60, K.65, G.66, A.68, T.69, R.84 Ligand excluded by PLIP NH4.3: 2 residues within 4Å: Chain A: D.58, Y.60 Ligand excluded by PLIP NH4.4: 2 residues within 4Å: Chain A: D.211, K.213 Ligand excluded by PLIP NH4.5: 4 residues within 4Å: Chain A: H.41, A.92, T.112, E.152 Ligand excluded by PLIP NH4.6: 2 residues within 4Å: Chain A: K.209 Ligands: MPD.7 Ligand excluded by PLIP NH4.16: 3 residues within 4Å: Chain B: S.7, P.8, R.22 Ligand excluded by PLIP NH4.17: 9 residues within 4Å: Chain B: N.93, S.94 Chain C: S.107, Q.109 Chain D: S.30, Y.33, G.93 Ligands: PO4.42, CL.46 Ligand excluded by PLIP NH4.18: 7 residues within 4Å: Chain B: Q.37, K.39, P.59, R.61, F.62, E.81, D.82 Ligand excluded by PLIP NH4.24: 3 residues within 4Å: Chain C: Y.27, T.28, Y.32 Ligand excluded by PLIP NH4.25: 5 residues within 4Å: Chain C: K.19, T.71, R.72, D.73, Y.80 Ligand excluded by PLIP NH4.26: 4 residues within 4Å: Chain C: K.228 Chain D: S.122, D.123, E.124 Ligand excluded by PLIP NH4.27: 5 residues within 4Å: Chain C: E.10, K.12, S.17, V.18, K.19 Ligand excluded by PLIP NH4.28: 3 residues within 4Å: Chain C: E.10, V.11, K.12 Ligand excluded by PLIP NH4.29: 10 residues within 4Å: Chain A: Y.50, D.58, G.59 Chain C: Y.102, G.104, G.105, D.106, S.107, P.108, D.110 Ligand excluded by PLIP NH4.30: 6 residues within 4Å: Chain C: S.141, S.142, K.143 Chain D: P.120, F.210 Ligands: CL.39 Ligand excluded by PLIP NH4.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NH4.40: 3 residues within 4Å: Chain B: T.27 Chain D: Q.27, S.28 Ligand excluded by PLIP

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 7 residues within 4Å: Chain A: A.202, H.203, P.204, S.207, T.208, K.209 Ligands: NH4.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.202 Water bridges: A:S.207 MPD.32: 7 residues within 4Å: Chain C: K.131, G.132, P.133, S.134, S.217, T.219, V.221 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.131, C:T.219, C:V.221 Hydrogen bonds: C:G.132

14 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 4 residues within 4Å: Chain A: P.122, P.123, T.208, V.210 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.122 PO4.9: 4 residues within 4Å: Chain A: H.168 Chain B: T.164, D.165, D.167 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.164, B:D.167, B:D.167 Water bridges: B:S.174, A:T.169 Salt bridges: A:H.168 PO4.10: 7 residues within 4Å: Chain A: Y.149, E.152, P.153, V.154, P.171, A.172, L.181 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.149, A:E.152, A:E.152, A:V.154, A:A.172 PO4.11: 4 residues within 4Å: Chain A: P.130, V.140, R.192, P.193 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.192 PO4.12: 6 residues within 4Å: Chain A: T.28, D.31, Y.32 Chain C: G.54, N.55, R.72 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.54 Water bridges: C:R.72, A:T.28, A:T.28 Salt bridges: C:R.72 PO4.19: 11 residues within 4Å: Chain A: L.145, P.171, V.173, T.180, L.181, S.182 Chain B: L.160, N.161, S.162, S.176, T.178 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.162, B:S.162, B:S.176, B:T.178, B:T.178, A:S.182 PO4.20: 12 residues within 4Å: Chain B: D.30, D.31, D.32, E.50, G.51 Chain C: W.47, K.59, Y.60, S.61, Q.62, Q.65 Chain D: S.95 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:Y.60, C:Y.60, C:Q.62, B:D.30, B:D.31, B:D.31, B:D.31, B:G.51 PO4.33: 2 residues within 4Å: Chain C: K.220, D.222 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.222 Salt bridges: C:K.220 PO4.34: 10 residues within 4Å: Chain C: F.180, P.181, V.183, S.191, L.192, S.193 Chain D: E.162, S.163, S.177, T.179 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.177, D:S.177, D:T.179, C:S.193, C:S.193 PO4.35: 11 residues within 4Å: Chain A: Y.33, Y.52, N.54, N.55 Chain C: S.31, Y.32, A.33, V.99, Y.102, N.111, Y.112 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.31, C:S.31, C:A.33, C:N.111, A:N.55 PO4.36: 5 residues within 4Å: Chain C: H.178, T.179 Chain D: T.165, E.166, D.168 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.178 PO4.41: 7 residues within 4Å: Chain C: P.101, Y.113, D.115 Chain D: Y.50, A.56, T.57 Ligands: CL.47 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.113, C:D.115, C:D.115, D:T.57 PO4.42: 9 residues within 4Å: Chain B: N.93 Chain D: S.28, V.29, S.30, Y.33, Q.91, G.93, S.94 Ligands: NH4.17 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.93 PO4.43: 8 residues within 4Å: Chain C: R.44, L.45, E.46, W.47, K.63 Chain D: Y.97, T.98, F.99 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.44, D:F.99 Water bridges: C:K.63, C:K.63 Salt bridges: C:K.63

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

CL.13: 2 residues within 4Å: Chain A: Q.1, G.26 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: Q.3, L.4, W.107, G.108 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: S.189 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: D.30 Chain C: K.63 Chain D: E.1, S.96 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: R.155, E.185, H.189 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain B: E.123 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain C: K.224 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain C: K.19, S.21 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain C: S.141, S.142 Ligands: NH4.30 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain D: V.151, Q.156, H.190 Ligand excluded by PLIP CL.45: 5 residues within 4Å: Chain D: R.143, A.145, E.162, V.164, L.176 Ligand excluded by PLIP CL.46: 5 residues within 4Å: Chain B: S.94 Chain C: S.107 Chain D: S.30, S.31 Ligands: NH4.17 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain C: D.115 Chain D: T.57 Ligands: PO4.41 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bancroft, T. et al., Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes. J.Exp.Med. (2019)

Release Date

2019-07-24

Peptides

ib3 Heavy Chain: A
ib3 Light Chain: B
iglb12 Heavy Chain: C
iglb12 Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

ib3 Heavy Chain

ib3 Light Chain

iglb12 Heavy Chain

iglb12 Light Chain