5MYQ

Crystal structure of avidin in complex with ferrocene homobiotin derivative

PDB DOI: https://doi.org/10.2210/pdb5MYQ/pdb

Classification: Biotin-binding protein
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2017-01-27 Released: 2018-02-14
Deposition Author(s): Strzelczyk, P., Bujacz, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.232
R-Value Work: 0.186
R-Value Observed: 0.187

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: 62.55 kDa
Atom Count: 4,346
Modelled Residue Count: 488
Deposited Residue Count: 512
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	128	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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HBF Query on HBF Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain S [auth C] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth D]	E [auth A], K [auth B], S [auth C], Z [auth D]	ferrocene homobiotin derivative C₂₁ H₁₇ Fe N₂ O S YYWARPGDAKPMLM-VZXRKJOKSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain Z [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C]	AA [auth D], F [auth A], L [auth B], T [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain L [auth B] Focus chain T [auth C]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.232
R-Value Work: 0.186
R-Value Observed: 0.187
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.933	α = 90
b = 82.081	β = 106.29
c = 74.601	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-02-14

Deposition Author(s):

Strzelczyk, P.

Bujacz, G.

Revision History (Full details and data files)

Version 1.0: 2018-02-14
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary