PDBsum entry 1uj3

Immune system/blood clotting

PDB id: 1uj3

Contents

Protein chains

214 a.a. *

217 a.a. *

205 a.a. *

Waters ×464

* Residue conservation analysis

PDB id:

1uj3

Name:

Immune system/blood clotting

Title:

Crystal structure of a humanized fab fragment of anti-tissue-factor antibody in complex with tissue factor

Structure:

Igg fab light chain. Chain: a. Fragment: anti-tissue-factor antibody hatr-5 fab. Engineered: yes. Igg fab heavy chain. Chain: b. Fragment: anti-tissue-factor antibody hatr-5 fab. Engineered: yes. Tissue factor.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Trimer (from PQS)

Resolution:

2.10Å R-factor: 0.196 R-free: 0.227

Authors:

U.Ohto,R.Mizutani,M.Nakamura,H.Adachi,Y.Satow

Key ref:

U.Ohto et al. (2004). Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor. J Synchrotron Radiat, 11, 105-108. PubMed id: 14646147

Date:

25-Jul-03 Release date: 25-Jul-04

Protein chain

No UniProt id for this chain

Struc: 214 a.a.

Protein chain

No UniProt id for this chain

Struc: 217 a.a.

Protein chain

P13726  (TF_HUMAN) -  Tissue factor from Homo sapiens

Seq: 295 a.a.

Struc: 205 a.a.

J Synchrotron Radiat 11:105-108 (2004)

PubMed id: 14646147

Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor.

U.Ohto, R.Mizutani, M.Nakamura, H.Adachi, Y.Satow.

ABSTRACT

Tissue factor (TF) is a membrane-anchored protein that initiates the extrinsic cascade of blood coagulation. TF forms a complex with serine protease Factor VIIa, and then activates Factor X zymogen to Factor Xa, leading to the blood coagulation. Humanized anti-TF antibody hATR-5 strongly inhibits TF-initiated blood coagulation, and is of potential use for various thrombotic diseases. The Fab fragment of antibody hATR-5 is obtained for crystallization. The crystal structure of the complex of the Fab with extracellular domains of human TF was determined with the molecular replacement method, and refined to an R factor of 0.196 at 2.1 A resolution. All the complementarity-determining regions (CDRs) of the Fab are involved in interaction with the C-terminal-side extracellular domain of TF through 19 hydrogen bonds. The interface between the Fab and TF molecules contains 15 water molecules, and yields buried surface areas as wide as 2000 A2. The TF surface in the interface is possibly involved in the activation of Factor X, by forming a transient ternary complex of Factor X-TF-Factor VIIa. Electrostatic interactions are predominantly observed between the heavy-chain CDRs and TF. These hydrogen-bonding and electrostatic interactions together with the wide buried areas contribute to the high affinity of the antibody toward TF, leading to the effective inhibition of the TF-initiated blood coagulation.