9CAM | pdb_00009cam

Aminopeptidase N close state

PDB DOI: https://doi.org/10.2210/pdb9CAM/pdb
EM Map EMD-45396: EMDB EMDataResource

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

Deposited: 2024-06-17 Released: 2025-08-06
Deposition Author(s): Lyu, M., Zhang, Z.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9CAM

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

Literature

Aminopeptidase N close state

Lyu, M., Zhang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 225.01 kDa
Atom Count: 14,945
Modeled Residue Count: 1,802
Deposited Residue Count: 1,934
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A [auth B], B [auth A]	967	Homo sapiens	Mutation(s): 0 EC: 3.4.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for P15144 (Homo sapiens) Explore P15144 Go to UniProtKB: P15144
PHAROS: P15144 GTEx: ENSG00000166825
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15144
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A [auth B] Focus chain B [auth A]	Go to GlyGen: P15144-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, I	3		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain I Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, J	2		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain H Focus chain J Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A]	K [auth B] M [auth B] N [auth B] O [auth A] Q [auth A] K [auth B], M [auth B], N [auth B], O [auth A], Q [auth A], R [auth A], S [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain L [auth B] MOL2 format, chain P [auth A] MOL2 format, chain L [auth B] mmCIF format, chain P [auth A] mmCIF format, chain L [auth B]	L [auth B], P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth A] Interactions & Density Focus chain L [auth B] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-08-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.