SMTL ID : 2dqt.1

High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CPD: [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER(Non-covalent)

CPD.1: 18 residues within 4Å: Chain A: H.31, S.32, F.94, G.96, S.97, V.99, P.101 Chain B: A.33, W.47, S.50, S.52, Y.58, V.98, H.100, D.102, G.103, W.107, F.109 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.58, A:V.99 Hydrogen bonds: B:S.50, B:Y.58, B:G.103, A:G.96 pi-Stacking: B:Y.58, B:H.100, B:W.107, B:W.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oda, M. et al., Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis. J.Mol.Biol. (2007)

Release Date

2006-06-20

Peptides

IMMUNOGLOBULIN 6D9: A
IMMUNOGLOBULIN 6D9: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

IMMUNOGLOBULIN 6D9

IMMUNOGLOBULIN 6D9

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