1NFB | pdb_00001nfb

Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with 6Cl-IMP and NAD

• PDB DOI: https://doi.org/10.2210/pdb1NFB/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: 2.90 Å
• R-Value Free: 
  0.274 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

The Conformation of NAD Bound to Human Inosine Monophosphate Dehydrogenase Type II

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 and generated by PISA,PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 113.81 kDa 
• Atom Count: 5,885 
• Modeled Residue Count: 792 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
CPR	C [auth A], E [auth B]	6-CHLOROPURINE RIBOSIDE, 5'-MONOPHOSPHATE C10 H13 Cl N4 O7 P ALOBOMYIOYNCBS-KQYNXXCUSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.274 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.19	α = 90
b = 145.19	β = 90
c = 127.1	γ = 90

Software Package:

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

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: Derived calculations, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary