SMTL ID : 1yei.3 (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: 4 residues within 4Å: Chain A: D.156, H.194 Ligands: ZN.6, ZN.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.156, A:H.194, H2O.3, H2O.4 ZN.2: 1 residues within 4Å: Ligands: ZN.4 No protein-ligand interaction detected (PLIP) ZN.3: 2 residues within 4Å: Chain A: H.54 Chain B: D.107 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.107, B:D.107, A:H.54, H2O.1, H2O.6 ZN.4: 2 residues within 4Å: Chain A: H.98 Ligands: ZN.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.98, H2O.1, H2O.3 ZN.5: 2 residues within 4Å: Ligands: ZN.6, ZN.7 No protein-ligand interaction detected (PLIP) ZN.6: 2 residues within 4Å: Ligands: ZN.1, ZN.5 No protein-ligand interaction detected (PLIP) ZN.7: 4 residues within 4Å: Chain A: D.156, N.195 Ligands: ZN.1, ZN.5 No protein-ligand interaction detected (PLIP) ZN.9: 4 residues within 4Å: Chain C: D.156, H.194 Ligands: ZN.14, ZN.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.156, C:H.194, H2O.9, H2O.9 ZN.10: 1 residues within 4Å: Ligands: ZN.12 No protein-ligand interaction detected (PLIP) ZN.11: 2 residues within 4Å: Chain C: H.54 Chain D: D.107 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.107, D:D.107, C:H.54, H2O.7, H2O.12 ZN.12: 2 residues within 4Å: Chain C: H.98 Ligands: ZN.10 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.98, H2O.7, H2O.9 ZN.13: 2 residues within 4Å: Ligands: ZN.14, ZN.15 No protein-ligand interaction detected (PLIP) ZN.14: 2 residues within 4Å: Ligands: ZN.9, ZN.13 No protein-ligand interaction detected (PLIP) ZN.15: 4 residues within 4Å: Chain C: D.156, N.195 Ligands: ZN.9, ZN.13 No protein-ligand interaction detected (PLIP)

2 x PGG: PARA-NITROPHENYLPHOSPHONOBUTANOYL-GLYCINE(Non-covalent)

PGG.8: 14 residues within 4Å: Chain A: Y.31, Y.37, N.39, V.94, G.96, F.99, Y.101, F.103 Chain B: H.35, V.37, W.47, W.99, F.101, Y.108 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.37, A:V.94, A:Y.101, A:Y.101, B:W.99, B:F.101 Hydrogen bonds: A:N.39, A:G.96, A:F.99, A:Y.101, B:W.99, B:Y.108 Water bridges: A:T.97 pi-Stacking: B:W.99 PGG.16: 14 residues within 4Å: Chain C: Y.31, Y.37, N.39, V.94, G.96, F.99, Y.101, F.103 Chain D: H.35, V.37, W.47, W.99, F.101, Y.108 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.37, C:V.94, C:Y.101, C:Y.101, D:W.99, D:F.101 Hydrogen bonds: C:N.39, C:G.96, C:F.99, D:W.99 Water bridges: C:T.97, C:Y.101 pi-Stacking: D:W.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gigant, B. et al., Crossreactivity, efficiency and catalytic specificity of an esterase-like antibody. J.Mol.Biol. (1998)

Release Date

1999-01-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
L

B
H

D
H

PROTEIN (IG ANTIBODY D2.3 (LIGHT CHAIN))

PROTEIN (IG ANTIBODY D2.3 (HEAVY CHAIN))

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