SMTL ID : 1yec.1 (1 other biounit)

STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

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

ZN.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 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: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.54, B:D.107, B:D.107, H2O.2, H2O.5 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.2, H2O.4 ZN.5: 3 residues within 4Å: Chain A: D.156, H.194 Ligands: 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.6: 2 residues within 4Å: Ligands: ZN.5, ZN.7 No protein-ligand interaction detected (PLIP) ZN.7: 1 residues within 4Å: Ligands: ZN.6 No protein-ligand interaction detected (PLIP)

1 x PNB: 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE(Non-covalent)

PNB.8: 17 residues within 4Å: Chain A: Y.31, Y.37, N.39, V.94, Q.95, G.96, F.99, Y.101, F.103 Chain B: H.35, V.37, W.47, T.97, W.99, F.101, Y.108, W.113 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.37, A:V.94, A:Y.101, B:F.101 Hydrogen bonds: A:N.39, A:G.96, A:Y.101, B:R.50, B:W.99, B:Y.108 Water bridges: A:Y.101 pi-Stacking: B:W.99, B:W.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Charbonnier, J.B. et al., Structural convergence in the active sites of a family of catalytic antibodies. Science (1997)

Release Date

1997-10-15

Peptides

IGG2A FAB FRAGMENT (D2.3): A
IGG2A FAB FRAGMENT (D2.3): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

IGG2A FAB FRAGMENT (D2.3)

IGG2A FAB FRAGMENT (D2.3)

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