2Z2D | pdb_00002z2d

Solution structure of human macrophage elastase (MMP-12) catalytic domain complexed with a gamma-keto butanoic acid inhibitor

PDB DOI: https://doi.org/10.2210/pdb2Z2D/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-05-18 Released: 2007-11-20
Deposition Author(s): Zheng, X., Ou, L.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 15
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 2Z2D

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

Literature

Solution structure of human macrophage elastase (MMP-12) catalytic domain complexed with a gamma-keto butanoic acid inhibitor

Zheng, X., Ou, L.

To be published.

Macromolecule Content

Total Structure Weight: 18.88 kDa
Atom Count: 1,273
Modeled Residue Count: 158
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	164	Homo sapiens	Mutation(s): 0 Gene Names: MMP12 EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900 Go to UniProtKB: P39900
PHAROS: P39900 GTEx: ENSG00000262406
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HSI Query on HSI Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	(3R)-3-{4-[(4-CHLOROPHENYL)ETHYNYL]BENZOYL}NONANOIC ACID C₂₄ H₂₅ Cl O₃ UOBFNJXLVSPHNN-OAQYLSRUSA-N		Interactions Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
HSI	BindingDB: 2Z2D	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 15
Selection Criteria: structures with the lowest energy

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2022-03-16
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-05-29
Changes: Data collection

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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.