3UVC | pdb_00003uvc

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 (Depositor), 0.178 (DCC)
R-Value Work:
0.130 (Depositor), 0.134 (DCC)
R-Value Observed:
0.132 (Depositor)

Starting Model: other
View more details

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
Modeled 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
PHAROS: 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] mmCIF 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 J [auth A] SDF format, chain O [auth A] SDF format, chain Z [auth B] SDF format, chain I [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain I [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain I [auth A]	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 D [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 C [auth A] MOL2 format, chain D [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 C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain C [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] mmCIF format, chain CA [auth B] mmCIF 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 X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain K [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain K [auth A]	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 L [auth A] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain AA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain AA [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 (Depositor), 0.178 (DCC)
R-Value Work: 0.130 (Depositor), 0.134 (DCC)
R-Value Observed: 0.132 (Depositor)

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

View Full Validation Report

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