9IWT | pdb_00009iwt

Crystal structure of human NAMPT complexed with AMP

PDB DOI: https://doi.org/10.2210/pdb9IWT/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Expression vector pET-mod
Mutation(s): No

Deposited: 2024-07-26 Released: 2025-06-11
Deposition Author(s): Wang, G., Wu, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human NAMPT complexed with AMP

Wang, G., Wu, C.

To be published.

Macromolecule Content

Total Structure Weight: 227.92 kDa
Atom Count: 16,029
Modeled Residue Count: 1,843
Deposited Residue Count: 1,988
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B, C, D	497	Homo sapiens	Mutation(s): 0 Gene Names: NAMPT, PBEF, PBEF1 EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens) Explore P43490 Go to UniProtKB: P43490
PHAROS: P43490 GTEx: ENSG00000105835
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], L [auth C], P [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] J [auth B] K [auth B] M [auth C] F [auth A], G [auth A], J [auth B], K [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain H [auth A] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain H [auth A] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain H [auth A]	H [auth A], O [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth C] Focus chain S [auth D]