5HLM | pdb_00005hlm

Crystal structure of avidin complex with a ferrocene biotin derivative

• PDB DOI: https://doi.org/10.2210/pdb5HLM/pdb

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


• Deposited: 2016-01-15 Released: 2017-01-18 
• Deposition Author(s): Strzelczyk, P., Bujacz, G.
• Funding Organization(s): National Science Centre

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Ferrocene-Biotin Conjugates: Synthesis, Structure, Cytotoxic Activity and Interaction with Avidin

Blauz, A., Rychlik, B., Makal, A., Szulc, K., Strzelczyk, P., Bujacz, G., Zakrzewski, J., Wozniak, K., Plazuk, D.

(2016) Chempluschem 81: 1191-1201

• DOI: https://doi.org/10.1002/cplu.201600320

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.99 kDa 
• Atom Count: 3,812 
• Modeled Residue Count: 461 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

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
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B9F	E [auth A], G [auth B], I [auth C], K [auth D]	[(1,2,3,4,5-eta)-cyclopentadienyl]{(1,2,3,4,5-eta)-1-[1-hydroxy-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentyl]cyclopentadienyl}iron C20 H26 Fe N2 O2 S ZYEYPNBFMRLUKC-MIZLAOAMSA-N
NAG	F [auth A], H [auth B], J [auth C], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.2	α = 90
b = 74.91	β = 106.17
c = 76.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Strzelczyk, P., Bujacz, G.

---

Funding Organization	Location	Grant Number
National Science Centre	Poland	DEC-2013/11/N/ST5/01296

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-09
  Changes: Structure summary