1NF7

Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with Ribavirin Monophosphate and C2-Mycophenolic Adenine Dinucleotide

• PDB DOI: https://doi.org/10.2210/pdb1NF7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-12-13 Released: 2004-01-27 
• Deposition Author(s): Risal, D., Strickler, M.D., Goldstein, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.277 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 

Literature

Crystal Structure of Human Inosine Monophosphate Dehydrogenase type II complexed with the MPA/NAD analog C2-MAD

Risal, D., Strickler, M.D., Goldstein, B.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 114.9 kDa 
• Atom Count: 7,114 
• Modelled Residue Count: 908 
• Deposited Residue Count: 1,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase 2	A, B	514	Homo sapiens	Mutation(s): 0  Gene Names: IMPDH2 EC: 1.1.1.205
UniProt & NIH Common Fund Data Resources
Find proteins for P12268 (Homo sapiens) Explore P12268  Go to UniProtKB:  P12268
PHAROS:  P12268 GTEx:  ENSG00000178035

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYD	E [auth A], H [auth B]	{[5-(6-AMINO-PURIN-7-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-[2-(4-HYDROXY-6-METHOXY-7-METHYL-3-OXO-1,3-DIHYDRO-ISOBENZOFURAN-5-YL)-ETHYL] ESTER C23 H29 N5 O13 P2 AMYUZLUBFKOUEX-JKWAKEATSA-N
RVP	D [auth A], G [auth B]	RIBAVIRIN MONOPHOSPHATE C8 H13 N4 O8 P SDWIOXKHTFOULX-AFCXAGJDSA-N
UNK	I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	UNKNOWN C4 H9 N O2 QWCKQJZIFLGMSD-VKHMYHEASA-N
K	C [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MYD	BindingDB:  1NF7	Ki: 250 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.277 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.58	α = 90
b = 146.58	β = 90
c = 128.92	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALA	data scaling
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-27 
Deposition Author(s): Risal, D., Strickler, M.D., Goldstein, B.M.

Revision History  

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description