8CHE

TLT-1 binding Fab of the bispecific antibody HMB-001 in complex with the TLT-1 stalk peptide

PDB DOI: https://doi.org/10.2210/pdb8CHE/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-02-07 Released: 2023-12-27
Deposition Author(s): Johansson, E., Schluckebier, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.174
R-Value Work: 0.157
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

HMB-001: A Novel Bispecific Antibody Accumulating and Targeting Endogenous FVIIa to Activated Platelets for Subcutaneous Prophylaxis in Multiple Bleeding Disorders Including Glanzmann Thrombasthenia.

Gandhi, P.S., Zivkovic, M., Oestergaard, H., Bonde, A.C., Loevgreen, M.N., Schluckebier, G., Johansson, E., Rea, C.J., Soerensen, B., Schutgens, R.E., Urbanus, R.T., Faber, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 102.04 kDa
Atom Count: 8,034
Modelled Residue Count: 896
Deposited Residue Count: 942
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	A [auth H], C [auth A]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	B [auth L], D [auth B]	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Trem-like transcript 1 protein	E [auth C], F [auth D]	37	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q86YW5 (Homo sapiens) Explore Q86YW5 Go to UniProtKB: Q86YW5
PHAROS: Q86YW5 GTEx: ENSG00000161911
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86YW5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.174
R-Value Work: 0.157
R-Value Observed: 0.157
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.234	α = 91.88
b = 65.377	β = 91.72
c = 67.145	γ = 92.89

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-27

Deposition Author(s):

Schluckebier, G.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-12-27
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.