SMTL ID : 4ong.1

Fab fragment of 3D6 in complex with amyloid beta 1-40

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

27 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 1 residues within 4Å: Chain A: D.213 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, H2O.1 ZN.2: 2 residues within 4Å: Chain A: D.62 Ligands: IMD.15 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.62, A:D.62, H2O.1, H2O.1 ZN.3: 4 residues within 4Å: Chain A: H.170 Chain B: N.143, D.172 Ligands: ZN.34 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.170, B:D.172, H2O.5, H2O.5 ZN.4: 3 residues within 4Å: Ligands: IMD.14, CL.16, CL.17 No protein-ligand interaction detected (PLIP) ZN.5: 2 residues within 4Å: Ligands: CL.18, CL.19 No protein-ligand interaction detected (PLIP) ZN.6: 1 residues within 4Å: Chain A: D.179 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.179, H2O.1 ZN.7: 5 residues within 4Å: Chain B: R.101 Chain C: D.1, A.2, E.3, F.4 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.3, H2O.8, H2O.8, H2O.10, H2O.10 ZN.8: 3 residues within 4Å: Chain A: K.65 Ligands: IMD.15, CL.20 No protein-ligand interaction detected (PLIP) ZN.9: 1 residues within 4Å: Chain C: F.4 No protein-ligand interaction detected (PLIP) ZN.10: 1 residues within 4Å: Chain A: T.113 No protein-ligand interaction detected (PLIP) ZN.11: 1 residues within 4Å: Chain A: K.214 No protein-ligand interaction detected (PLIP) ZN.12: 2 residues within 4Å: Chain A: R.44, E.46 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.46, H2O.1, H2O.3 ZN.13: 2 residues within 4Å: Chain A: S.61, D.62 No protein-ligand interaction detected (PLIP) ZN.21: 1 residues within 4Å: Chain B: H.98 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.98 ZN.22: 3 residues within 4Å: Chain B: H.194 Ligands: CL.39, CL.40 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.194, H2O.10 ZN.23: 1 residues within 4Å: Chain B: D.115 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.115, B:D.115, H2O.5 ZN.24: 3 residues within 4Å: Chain B: H.203 Ligands: CL.36, CL.37 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.203, H2O.5 ZN.25: 1 residues within 4Å: Ligands: IMD.35 No protein-ligand interaction detected (PLIP) ZN.26: 2 residues within 4Å: Chain B: D.170 Ligands: CL.38 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.170, H2O.5, H2O.5 ZN.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.28: 2 residues within 4Å: Chain B: K.154, E.200 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.200, B:E.200, H2O.9, H2O.10 ZN.29: 2 residues within 4Å: Chain B: R.66, E.84 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.84, H2O.6 ZN.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.31: 3 residues within 4Å: Chain B: G.157, S.196 Ligands: CL.41 No protein-ligand interaction detected (PLIP) ZN.32: 2 residues within 4Å: Chain B: N.143, D.175 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.175 ZN.33: 2 residues within 4Å: Chain B: D.31 Chain C: R.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.31, B:D.31, H2O.5 ZN.34: 6 residues within 4Å: Chain A: H.170 Chain B: N.143, D.172, T.177, S.179 Ligands: ZN.3 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.170, B:D.172, H2O.5, H2O.5

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.14: 6 residues within 4Å: Chain A: S.209, T.210, K.211 Ligands: ZN.4, CL.16, CL.17 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:K.211 IMD.15: 7 residues within 4Å: Chain A: Y.60, D.62, K.65 Chain B: F.99 Ligands: ZN.2, ZN.8, CL.20 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:F.99 IMD.35: 5 residues within 4Å: Chain A: D.42 Chain B: L.9, G.105, G.106 Ligands: ZN.25 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:K.108, A:D.42

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

CL.16: 8 residues within 4Å: Chain A: A.204, H.205, P.206, T.210, K.211 Ligands: ZN.4, IMD.14, CL.17 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain A: P.206, S.209 Ligands: ZN.4, IMD.14, CL.16 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: N.161, S.162, N.202 Ligands: ZN.5, CL.19 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: N.202, D.213 Ligands: ZN.5, CL.18 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: Y.59, Y.60, K.65 Ligands: ZN.8, IMD.15 Ligand excluded by PLIP CL.36: 6 residues within 4Å: Chain B: D.115, A.116, A.117, H.203 Ligands: ZN.24, CL.37 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain B: P.118, T.202, H.203 Ligands: ZN.24, CL.36 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain B: G.89, L.90, D.170 Ligands: ZN.26 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain B: R.193, H.194 Ligands: ZN.22, CL.40 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain B: R.160, E.190, H.194 Ligands: ZN.22, CL.39 Ligand excluded by PLIP CL.41: 6 residues within 4Å: Chain B: K.154, D.156, G.157, S.196, T.198 Ligands: ZN.31 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feinberg, H. et al., Crystal structure reveals conservation of amyloid-beta conformation recognized by 3D6 following humanization to bapineuzumab. Alzheimers Res Ther (2014)

Release Date

2014-06-11

Peptides

3D6 FAB ANTIBODY HEAVY CHAIN: A
3D6 FAB ANTIBODY LIGHT CHAIN: B
Amyloid beta A4 protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
P

3D6 FAB ANTIBODY HEAVY CHAIN

3D6 FAB ANTIBODY LIGHT CHAIN

Amyloid beta A4 protein

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