1N0X | pdb_00001n0x

Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope

• PDB DOI: https://doi.org/10.2210/pdb1N0X/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2002-10-15 Released: 2004-04-13 
• Deposition Author(s): Saphire, E.O., Montero, M., Menendez, A., Irving, M.B., Zwick, M.B., Parren, P.W.H.I., Burton, D.R., Scott, J.K., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope

Saphire, E.O., Montero, M., Menendez, A., Irving, M.B., Zwick, M.B., Parren, P.W.H.I., Burton, D.R., Scott, J.K., Wilson, I.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 103.77 kDa 
• Atom Count: 7,899 
• Modeled Residue Count: 917 
• Deposited Residue Count: 932 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN LIGHT CHAIN	A [auth L], C [auth M]	215	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN HEAVY CHAIN	B [auth H], D [auth K]	230	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
B2.1 peptide	E [auth P], F [auth R]	21	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	I [auth H]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
SO4	H, N [auth K], S [auth R], T [auth R]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth L], J [auth H], K [auth H], L [auth M], M, O [auth K], P [auth K], Q [auth K]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	R [auth P]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ORN	E [auth P], F [auth R]	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.621	α = 90
b = 184.358	β = 103.05
c = 56.173	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-13 
Deposition Author(s): Saphire, E.O., Montero, M., Menendez, A., Irving, M.B., Zwick, M.B., Parren, P.W.H.I., Burton, D.R., Scott, J.K., Wilson, I.A.

Revision History  

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-06-21
  Changes: Advisory, Database references, Experimental preparation, Source and taxonomy, Structure summary
• Version 1.4: 2025-03-26
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary