5MYQ | pdb_00005myq

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 (Depositor), 0.241 (DCC)
R-Value Work:
0.186 (Depositor), 0.195 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural investigation of the interactions of ferrocene homobiotin derivative with avidin.

Strzelczyk, P., Plazuk, D., Bujacz, G.

To be published.

Macromolecule Content

Total Structure Weight: 62.55 kDa
Atom Count: 4,346
Modeled Residue Count: 488
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth C] mmCIF 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] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF 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] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF 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 (Depositor), 0.241 (DCC)
R-Value Work: 0.186 (Depositor), 0.195 (DCC)
R-Value Observed: 0.187 (Depositor)

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

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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
Version 1.3: 2024-11-13
Changes: Structure summary