6XSN

Crystal structure of NHP VD20.5A4 Fab in complex with 16055 V1V2 1FD6 scaffold

PDB DOI: https://doi.org/10.2210/pdb6XSN/pdb

Classification: IMMUNE SYSTEM
Organism(s): Macaca mulatta
Mutation(s): No

Deposited: 2020-07-15 Released: 2021-07-21
Deposition Author(s): Aljedani, S., Pancera, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free: 0.267
R-Value Work: 0.221
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 63.53 kDa
Atom Count: 3,644
Modelled Residue Count: 476
Deposited Residue Count: 579
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VD20.5A4_heavy_chain	A [auth H]	224	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VD20.5A4_light_chain	B [auth L]	214	Macaca mulatta	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
16055_V1V2-1FD6	C	141	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C]	L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain G [auth L] SDF format, chain J [auth L] SDF format, chain H [auth L] MOL2 format, chain E [auth H] MOL2 format, chain G [auth L] MOL2 format, chain J [auth L] MOL2 format, chain H [auth L]	E [auth H], G [auth L], H [auth L], J [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain G [auth L] Focus chain H [auth L] Focus chain J [auth L] Interactions & Density Focus chain E [auth H] Focus chain G [auth L] Focus chain H [auth L] Focus chain J [auth L]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain I [auth L] SDF format, chain F [auth L] MOL2 format, chain D [auth H] MOL2 format, chain I [auth L] MOL2 format, chain F [auth L]	D [auth H], F [auth L], I [auth L]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain D [auth H] Focus chain F [auth L] Focus chain I [auth L] Interactions & Density Focus chain D [auth H] Focus chain F [auth L] Focus chain I [auth L]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth L] MOL2 format, chain K [auth L]	K [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth L] Interactions & Density Focus chain K [auth L]