6MHM

Crystal structure of human acid ceramidase in covalent complex with carmofur

PDB DOI: https://doi.org/10.2210/pdb6MHM/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): Yes

Deposited: 2018-09-18 Released: 2019-01-23
Deposition Author(s): Dementiev, A., Joachimiak, A., Doan, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

Currently 6MHM does not have a validation slider image.

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 92.45 kDa
Atom Count: 6,208
Modelled Residue Count: 734
Deposited Residue Count: 768
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acid ceramidase subunit alpha	A, C	131	Homo sapiens	Mutation(s): 2 Gene Names: ASAH1, ASAH, HSD-33, HSD33 EC: 3.5.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q13510 (Homo sapiens) Explore Q13510 Go to UniProtKB: Q13510
PHAROS: Q13510 GTEx: ENSG00000104763
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13510
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acid ceramidase subunit beta	B, D	253	Homo sapiens	Mutation(s): 1 Gene Names: ASAH1, ASAH, HSD-33, HSD33 EC: 3.5.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q13510 (Homo sapiens) Explore Q13510 Go to UniProtKB: Q13510
PHAROS: Q13510 GTEx: ENSG00000104763
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13510
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	3		N-Glycosylation	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D]	L [auth B], T [auth D], U [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth B] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain L [auth B] Focus chain T [auth D] Focus chain U [auth D]
JRY Query on JRY Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth D] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D]	M [auth B], V [auth D]	hexylcarbamic acid C₇ H₁₅ N O₂ YAQPZDICKJDHTR-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain V [auth D] Interactions & Density Focus chain M [auth B] Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	I [auth A] J [auth A] K [auth A] N [auth B] O [auth B] I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	E, G	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.218
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.718	α = 90
b = 68.65	β = 120.73
c = 98.386	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Currently 6MHM does not have a validation slider image.

Entry History

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Dementiev, A.

Joachimiak, A.

Doan, N.

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2019-04-24
Changes: Advisory, Data collection, Database references, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

6MHM

Crystal structure of human acid ceramidase in covalent complex with carmofur

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2