PDBsum entry 4m7k

Immune system

PDB id: 4m7k

Contents

Protein chains

220 a.a.

229 a.a.

Ligands

ACT

Metals

_CA

Waters ×347

PDB id:

4m7k

Name:

Immune system

Title:

Crystal structure of anti-tissue factor antibody 10h10

Structure:

10h10 light chain. Chain: l. Fragment: see remark 999. Engineered: yes. 10h10 heavy chain. Chain: h. Fragment: fd, see remark 999. Engineered: yes

Source:

Mus musculus, homo sapiens. Mouse, human. Organism_taxid: 10090, 9606. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek 293. Expression_system_cell_line: hek 293

Resolution:

1.90Å R-factor: 0.206 R-free: 0.243

Authors:

A.Teplyakov,G.Obmolova,T.Malia,G.L.Gilliland

Key ref:

A.Teplyakov et al. (2014). Antibody modeling assessment II. Structures and models. Proteins, 82, 1563-1582. PubMed id: 24633955 DOI: 10.1002/prot.24554

Date:

12-Aug-13 Release date: 26-Mar-14

Protein chain

No UniProt id for this chain

Struc: 220 a.a.

Protein chain

No UniProt id for this chain

Struc: 229 a.a.

DOI no: 10.1002/prot.24554

Proteins 82:1563-1582 (2014)

PubMed id: 24633955

Antibody modeling assessment II. Structures and models.

A.Teplyakov, J.Luo, G.Obmolova, T.J.Malia, R.Sweet, R.L.Stanfield, S.Kodangattil, J.C.Almagro, G.L.Gilliland.

ABSTRACT

To assess the state-of-the-art in antibody structure modeling, a blinded study was conducted. Eleven unpublished Fab crystal structures were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. In the first round, each participant submitted three non-ranked complete Fv models for each target. In the second round, CDR-H3 modeling was performed in the context of the correct environment provided by the crystal structures with CDR-H3 removed. In this report we describe the reference structures and present our assessment of the models. Some of the essential sources of errors in the predictions were traced to the selection of the structure template, both in terms of the CDR canonical structures and VL/VH packing. On top of this, the errors present in the Protein Data Bank structures were sometimes propagated in the current models, which emphasized the need for the curated structural database devoid of errors. Modeling non-canonical structures, including CDR-H3, remains the biggest challenge for antibody structure prediction. Proteins 2014; 82:1563-1582. © 2014 Wiley Periodicals, Inc.