7ZN1

Avidin + Biotin-Tempo

PDB DOI: https://doi.org/10.2210/pdb7ZN1/pdb

Classification: PROTEIN BINDING
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2022-04-20 Released: 2023-05-10
Deposition Author(s): Milani, J., Lau, K., Pojer, F., Ansermet, J.P., Saenz, F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.279
R-Value Work: 0.226
R-Value Observed: 0.229

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Avidin + Biotin-Tempo

Milani, J., Lau, K., Pojer, F., Ansermet, J.P., Saenz, F.

To be published.

Macromolecule Content

Total Structure Weight: 70.24 kDa
Atom Count: 3,923
Modelled Residue Count: 472
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avidin	A, B, C, D	152	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P02701 (Gallus gallus) Explore P02701 Go to UniProtKB: P02701
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02701
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KFL (Subject of Investigation/LOI) Query on KFL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D]	G [auth A], L [auth B], N [auth C], S [auth D]	6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide C₂₀ H₃₆ N₄ O₃ S PUXBASNOQZMIKI-ZOBUZTSGSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain S [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth D]	F [auth A], K [auth B], R [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C]	H [auth A], I [auth A], O [auth C], P [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	J [auth A], M [auth B], Q [auth C], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D]