9L2D | pdb_00009l2d

Structure of SARM1 bound to M1 in the intermediate state 1

PDB DOI: https://doi.org/10.2210/pdb9L2D/pdb
EM Map EMD-62772: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-12-17 Released: 2025-03-12
Deposition Author(s): Huang, Y., Zhang, J., Zheng, S., Wang, X.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.83 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Stepwise Activation of SARM1 by a Biosynthetic NMN mimic

Huang, Y., Zhang, J., Zheng, S., Wang, X.

To be published.

Macromolecule Content

Total Structure Weight: 646.46 kDa
Atom Count: 37,836
Modeled Residue Count: 4,800
Deposited Residue Count: 5,856
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(+) hydrolase SARM1	A, B, C, D, E A, B, C, D, E, F, G, H	732	Homo sapiens	Mutation(s): 0 Gene Names: SARM1, KIAA0524, SAMD2, SARM EC: 3.2.2.6 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6SZW1 (Homo sapiens) Explore Q6SZW1 Go to UniProtKB: Q6SZW1
PHAROS: Q6SZW1 GTEx: ENSG00000004139
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6SZW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EIV (Subject of Investigation/LOI) Query on A1EIV Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth G] mmCIF format, chain P [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(3-sulfanylpyridin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate C₁₀ H₁₅ N O₇ P S VITCWSBGSROZMF-ZYUZMQFOSA-O		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]