3D5H | pdb_00003d5h

Crystal structure of haementhin from Haemanthus multiflorus at 2.0A resolution: Formation of a novel loop on a TIM barrel fold and its functional significance

• PDB DOI: https://doi.org/10.2210/pdb3D5H/pdb

• Classification: PROTEIN BINDING
• Organism(s): Scadoxus multiflorus
• Mutation(s): No 


• Deposited: 2008-05-16 Released: 2009-03-31 
• Deposition Author(s): Kumar, S., Singh, N., Sinha, M., Singh, S.B., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.186 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.152 (Depositor) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of haementhin from Haemanthus multiflorus at 2.0A resolution: Formation of a novel loop on a TIM barrel fold and its functional significance

Kumar, S., Singh, N., Sinha, M., Singh, S.B., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 29.97 kDa 
• Atom Count: 2,417 
• Modeled Residue Count: 272 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haementhin	A	272	Scadoxus multiflorus	Mutation(s): 0  EC: 3.2.1.14
UniProt
Find proteins for B2ZGS7 (Scadoxus multiflorus) Explore B2ZGS7  Go to UniProtKB:  B2ZGS7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.186 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.152 (Depositor) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.803	α = 90
b = 65.4	β = 102
c = 49.435	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Kumar, S., Singh, N., Sinha, M., Singh, S.B., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary