2Z2T | pdb_00002z2t

Crystal structure of the complex between gp41 fragment N36 and fusion inhibitor SC34EK

• PDB DOI: https://doi.org/10.2210/pdb2Z2T/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate LW123)
• Mutation(s): No 


• Deposited: 2007-05-28 Released: 2008-06-03 
• Deposition Author(s): Nakamura, S., Ohkubo, T., Kobayashi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Intrahelical Salt-bridges in a-Helical Peptide Enhances its Binding to the Target: A New Design for HIV-1 Fusion Inhibitors

Nishikawa, H., Nakamura, S., Kodama, E., Ito, S., Kajiwara, K., Izumi, K., Sakagami, Y., Oishi, S., Ohkubo, T., Kobayashi, Y., Fujii, N., Matsuoka, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 26.02 kDa 
• Atom Count: 2,010 
• Modeled Residue Count: 222 
• Deposited Residue Count: 222 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp41 fragment N36	A, B, C	38	N/A	Mutation(s): 0
UniProt
Find proteins for Q70626 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123)) Explore Q70626  Go to UniProtKB:  Q70626

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion inhibitor peptide SC34EK	D, E, F	36	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	G [auth C]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE	D, E, F	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.014	α = 90
b = 105.014	β = 90
c = 78.308	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Nakamura, S., Ohkubo, T., Kobayashi, Y.

Revision History  

• Version 1.0: 2008-06-03
  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: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-23
  Changes: Structure summary