3UVC

MMP12 in a complex with the dimeric adduct: 5-(5-phenylhydantoin)-5-phenylhydantoin

PDB DOI: https://doi.org/10.2210/pdb3UVC/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-11-29 Released: 2013-01-02
Deposition Author(s): Derbyshire, D.J., Danielson, H., Nystrum, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.174
R-Value Work: 0.130
R-Value Observed: 0.132

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Characterization of fragments interacting with MMP-12

Nordstrom, H., Gossas, T., Derbyshire, D.J., Danielson, H.

To be published.

Macromolecule Content

Total Structure Weight: 38.27 kDa
Atom Count: 3,196
Modelled Residue Count: 317
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A, B	164	Homo sapiens	Mutation(s): 1 Gene Names: 4321, HME, MMP12 EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900 Go to UniProtKB: P39900
GTEx: ENSG00000262406
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0D2 Query on 0D2 Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	(4R,4'S)-4,4'-diphenyl-4,4'-biimidazolidine-2,2',5,5'-tetrone C₁₈ H₁₄ N₄ O₄ ZRUGFCSNTLNZEL-HDICACEKSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth A] SDF format, chain Z [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth B]	BA [auth B], I [auth A], J [auth A], O [auth A], Z [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth A] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth A] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain H [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain D [auth A]	C [auth A] D [auth A] H [auth A] T [auth B] U [auth B] C [auth A], D [auth A], H [auth A], T [auth B], U [auth B], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain Q [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain Q [auth A]	CA [auth B], Q [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain CA [auth B] Focus chain Q [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	E [auth A] F [auth A] G [auth A] K [auth A] V [auth B] E [auth A], F [auth A], G [auth A], K [auth A], V [auth B], W [auth B], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	AA [auth B] L [auth A] M [auth A] N [auth A] R [auth B] AA [auth B], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain AA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.174
R-Value Work: 0.130
R-Value Observed: 0.132
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.746	α = 90
b = 60.625	β = 103.1
c = 58.403	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-02

Deposition Author(s):

Derbyshire, D.J.

Danielson, H.

Nystrum, S.

Revision History (Full details and data files)

Version 1.0: 2013-01-02
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-04-03
Changes: Refinement description