SMTL ID : 1kn4.2 (3 other biounits)

CATALYTIC ANTIBODY D2.3 COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

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

ZN.1: 3 residues within 4Å: Chain A: H.54, K.58 Chain B: D.107 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.54, B:D.107, B:D.107, H2O.5 ZN.2: 2 residues within 4Å: Chain A: H.98 Ligands: ZN.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.98, H2O.1, H2O.1 ZN.3: 4 residues within 4Å: Chain A: D.156, H.194 Ligands: ZN.5, ZN.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.156, A:H.194, H2O.2, H2O.2 ZN.4: 2 residues within 4Å: Ligands: ZN.5, ZN.6 No protein-ligand interaction detected (PLIP) ZN.5: 2 residues within 4Å: Ligands: ZN.3, ZN.4 No protein-ligand interaction detected (PLIP) ZN.6: 3 residues within 4Å: Chain A: R.193 Ligands: ZN.3, ZN.4 No protein-ligand interaction detected (PLIP) ZN.7: 1 residues within 4Å: Ligands: ZN.2 No protein-ligand interaction detected (PLIP) ZN.9: 3 residues within 4Å: Chain C: H.54, K.58 Chain D: D.107 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:H.54, D:D.107, D:D.107, H2O.11 ZN.10: 2 residues within 4Å: Chain C: H.98 Ligands: ZN.15 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.98, H2O.6, H2O.7 ZN.11: 4 residues within 4Å: Chain C: D.156, H.194 Ligands: ZN.13, ZN.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.156, C:H.194, H2O.8, H2O.8 ZN.12: 2 residues within 4Å: Ligands: ZN.13, ZN.14 No protein-ligand interaction detected (PLIP) ZN.13: 2 residues within 4Å: Ligands: ZN.11, ZN.12 No protein-ligand interaction detected (PLIP) ZN.14: 3 residues within 4Å: Chain C: R.193 Ligands: ZN.11, ZN.12 No protein-ligand interaction detected (PLIP) ZN.15: 1 residues within 4Å: Ligands: ZN.10 No protein-ligand interaction detected (PLIP)

2 x PDE: PARA-NITROPHENYL PHOSPHONOBUTANOYL D-ALANINE(Non-covalent)

PDE.8: 14 residues within 4Å: Chain A: Y.37, N.39, V.94, G.96, F.99, Y.101, F.103 Chain B: H.35, V.37, W.47, R.50, W.99, F.101, Y.108 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:W.99, B:F.101, A:Y.37, A:V.94, A:F.99, A:Y.101, A:Y.101 Hydrogen bonds: B:W.99, B:Y.108, A:N.39, A:G.96, A:Y.101, A:Y.101 Salt bridges: B:R.50 pi-Stacking: B:W.99 PDE.16: 14 residues within 4Å: Chain C: Y.37, N.39, V.94, G.96, F.99, Y.101, F.103 Chain D: H.35, V.37, W.47, R.50, W.99, F.101, Y.108 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:Y.37, C:V.94, C:F.99, C:Y.101, C:Y.101, D:W.99, D:F.101 Hydrogen bonds: C:N.39, C:G.96, C:Y.101, D:W.99 Water bridges: C:Y.101 Salt bridges: D:R.50 pi-Stacking: D:W.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

D'Souza, L.J. et al., Remarkable remote chiral recognition in a reaction mediated by a catalytic antibody. J.Am.Chem.Soc. (2002)

Release Date

2002-03-13

Peptides

IG ANTIBODY D2.3 (LIGHT CHAIN): AC
IG ANTIBODY D2.3 (HEAVY CHAIN): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
L

B
H

D
H

IG ANTIBODY D2.3 (LIGHT CHAIN)

IG ANTIBODY D2.3 (HEAVY CHAIN)

Related Entries With Identical Sequence