3G5C

Structural and biochemical studies on the ectodomain of human ADAM22

PDB DOI: https://doi.org/10.2210/pdb3G5C/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2009-02-04 Released: 2009-08-18
Deposition Author(s): Liu, H., Shim, A., Chen, X., He, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.273
R-Value Work: 0.245

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural and biochemical studies on the ectodomain of human ADAM22

Liu, H., Shim, A., Chen, X., He, X.

(2009) J Biol Chem

Macromolecule Content

Total Structure Weight: 114.06 kDa
Atom Count: 7,915
Modelled Residue Count: 972
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAM 22	A, B	510	Homo sapiens	Mutation(s): 0 Gene Names: ADAM22, MDC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0K1 (Homo sapiens) Explore Q9P0K1 Go to UniProtKB: Q9P0K1
PHAROS: Q9P0K1 GTEx: ENSG00000008277
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9P0K1
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9P0K1-1
Sequence Annotations Expand
Reference Sequence

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 C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] I [auth B] J [auth B] C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	F [auth A] G [auth A] H [auth A] L [auth B] M [auth B] F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.273
R-Value Work: 0.245
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.09	α = 90
b = 122.09	β = 90
c = 208.69	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
SOLVE	phasing
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3G5C

Structural and biochemical studies on the ectodomain of human ADAM22

Structural and biochemical studies on the ectodomain of human ADAM22

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)