8BJZ | pdb_00008bjz

crystal structure of antibody Fab with SiaLac-amidine-Lys

PDB DOI: https://doi.org/10.2210/pdb8BJZ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-11-08 Released: 2023-09-27
Deposition Author(s): Moynie, L., Naismith, J.H.
Funding Organization(s): UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

crystal structure of antibody Fab with SiaLac-amidine-Lys

Moynie, L., Naismith, J.H., Sattentau, Q., Deimel, L., Khan, A., Davis, B., Baldwin, A., Buchanan, C.

To be published.

Macromolecule Content

Total Structure Weight: 99.09 kDa
Atom Count: 7,047
Modeled Residue Count: 857
Deposited Residue Count: 892
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BAR-1 Fab heavy chain	A [auth H], C [auth A]	227	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BAR-1 Fab light chain	B [auth L], D [auth B]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	E [auth C], F [auth D]	3		N/A	Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]
Glycosylation Resources
GlyTouCan: G91237TK GlyCosmos: G91237TK GlyGen: G91237TK

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SL9 (Subject of Investigation/LOI) Query on SL9 Download Ideal Coordinates CCD File SDF format, chain N [auth L] SDF format, chain U [auth B] MOL2 format, chain N [auth L] MOL2 format, chain U [auth B] mmCIF format, chain N [auth L] mmCIF format, chain U [auth B]	N [auth L], U [auth B]	(2~{S})-2-acetamido-6-(2-sulfanylethanimidoylamino)hexanamide C₁₀ H₂₀ N₄ O₂ S VZQPDVWZAWZPHB-QMMMGPOBSA-N		Interactions Focus chain N [auth L] Focus chain U [auth B] Interactions & Density Focus chain N [auth L] Focus chain U [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain H SDF format, chain P [auth A] MOL2 format, chain H MOL2 format, chain P [auth A] mmCIF format, chain H mmCIF format, chain P [auth A]	H, P [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain H Focus chain P [auth A] Interactions & Density Focus chain H Focus chain P [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain K [auth L] MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain K [auth L] mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain K [auth L]	I [auth H], J [auth H], K [auth L], Q [auth A], R [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth L] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth L] Focus chain Q [auth A] Focus chain R [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain L SDF format, chain M [auth L] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain O [auth A] MOL2 format, chain G [auth H] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] mmCIF format, chain G [auth H] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain O [auth A]	G [auth H] L M [auth L] O [auth A] S [auth B] G [auth H], L, M [auth L], O [auth A], S [auth B], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain L Focus chain M [auth L] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain G [auth H] Focus chain L Focus chain M [auth L] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002443 Query on PRD_002443	E [auth C], F [auth D]	SiaLac-amidine-Lys	Oligosaccharide /		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]