8P2T | pdb_00008p2t

Bovine naive ultralong antibody AbD08* collected at 100K

PDB DOI: https://doi.org/10.2210/pdb8P2T/pdb

Classification: IMMUNE SYSTEM
Organism(s): Bos taurus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-05-16 Released: 2024-07-10
Deposition Author(s): Clarke, J.D., Douangamath, A., Mikolajek, H., Stuart, D.I., Owens, R.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.206 (Depositor), 0.208 (DCC)
R-Value Work:
0.148 (Depositor), 0.148 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

The impact of chain-exchange on bovine ultralong immunoglobulins.

Clarke, J.D., Douangamath, A., Mikolajek, H., Placido, M.B.D., Stuart, D.I., Hammond, J., Owens, R.J.

(2024) Acta Crystallographica Section F

Macromolecule Content

Total Structure Weight: 57.5 kDa
Atom Count: 4,132
Modeled Residue Count: 483
Deposited Residue Count: 546
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody D08* heavy chain	A [auth H]	307	Bos taurus	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody D08* light chain	B [auth L]	239	Bos taurus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H] mmCIF format, chain C [auth H]	C [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Interactions & Density Focus chain C [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.206 (Depositor), 0.208 (DCC)
R-Value Work: 0.148 (Depositor), 0.148 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.03	α = 90
b = 70.86	β = 90
c = 96.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
pointless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Douangamath, A.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M011224/1

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.