1NF7 | pdb_00001nf7

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.277 (Depositor), 0.276 (DCC)
R-Value Work:
0.238 (Depositor), 0.258 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12268
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYD Query on MYD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	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		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
RVP Query on RVP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	RIBAVIRIN MONOPHOSPHATE C₈ H₁₃ N₄ O₈ P SDWIOXKHTFOULX-AFCXAGJDSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
UNL Query on UNL Download Ideal Coordinates CCD File	I [auth B] J [auth B] K [auth B] L [auth B] M [auth B] 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 ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

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 (Depositor), 0.276 (DCC)
R-Value Work: 0.238 (Depositor), 0.258 (DCC)
R-Value Observed: 0.238 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-01-27

Deposition Author(s):

Risal, D.

Strickler, M.D.

Goldstein, B.M.

Revision History (Full details and data files)

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
Version 2.0: 2025-02-12
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary

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Deposit Data

Help and Resources

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations