4H49 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A TWIN INHIBITOR.

Authors :   C. Antoni, E. A. Stura, L. Vera, E. Nuti, L. Carafa, E. Cassar-Lajeuness A. Rossello

Date :   17 Sep 12 (Deposition) - 24 Apr 13 (Release) - 12 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.16

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Divalent Inhibitor, Carboxylic Twin Inhibitor, Dimerisation, Metzincin, Zinc Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Antoni, L. Vera, L. Devel, M. P. Catalani, B. Czarny, E. Cassar-Lajeunesse, E. Nuti, A. Rossello, V. Dive, E. A. Stura
Crystallization Of Bi-Functional Ligand Protein Complexes.
J. Struct. Biol. V. 182 246 2013
PubMed-ID: 23567804 | Reference-DOI: 10.1016/J.JSB.2013.03.015

Molecule 1 - MACROPHAGE METALLOELASTASE
	Chains	:	A, B, C, D
	EC Number	:	3.4.24.65
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	HUMAN MMP12 CATALYTIC DOMAIN
	Gene	:	HME, MMP12
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MME, MACROPHAGE ELASTASE, ME, HME, MATRIX METALLOPROTEINASE- 12, MMP-12

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 30)

No.	Name	Count	Type	Full Name
1	CA	12	Ligand/Ion	CALCIUM ION
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	1	Ligand/Ion	GLYCEROL
4	L29	2	Ligand/Ion	N,N'-BIS(2-{(BIPHENYL-4-YLSULFONYL)[(2R)-1-(HYDROXYAMINO)-3-METHYL-1-OXOBUTAN-2-YL]AMINO}ETHYL)BENZENE-1,3-DICARBOXAMIDE (NON-PREFERRED NAME)
5	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	PGO	2	Ligand/Ion	S-1,2-PROPANEDIOL
7	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (5, 7)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	1	Ligand/Ion	GLYCEROL
4	L29	1	Ligand/Ion	N,N'-BIS(2-{(BIPHENYL-4-YLSULFONYL)[(2R)-1-(HYDROXYAMINO)-3-METHYL-1-OXOBUTAN-2-YL]AMINO}ETHYL)BENZENE-1,3-DICARBOXAMIDE (NON-PREFERRED NAME)
5	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	PGO	2	Ligand/Ion	S-1,2-PROPANEDIOL
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	-1	Ligand/Ion	GLYCEROL
4	L29	1	Ligand/Ion	N,N'-BIS(2-{(BIPHENYL-4-YLSULFONYL)[(2R)-1-(HYDROXYAMINO)-3-METHYL-1-OXOBUTAN-2-YL]AMINO}ETHYL)BENZENE-1,3-DICARBOXAMIDE (NON-PREFERRED NAME)
5	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	PGO	-1	Ligand/Ion	S-1,2-PROPANEDIOL
7	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:218 , HIS A:222 , HIS A:228 , L29 B:601	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196	BINDING SITE FOR RESIDUE ZN A 302
03	AC3	SOFTWARE	ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:431 , HOH A:432	BINDING SITE FOR RESIDUE CA A 303
04	AC4	SOFTWARE	ASP A:124 , GLU A:199 , GLU A:201 , HOH A:408 , HOH A:409	BINDING SITE FOR RESIDUE CA A 304
05	AC5	SOFTWARE	ASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201	BINDING SITE FOR RESIDUE CA A 305
06	AC6	SOFTWARE	GLY A:166 , ALA A:167 , DMS A:307	BINDING SITE FOR RESIDUE PGO A 306
07	AC7	SOFTWARE	ARG A:165 , HIS A:168 , PGO A:306	BINDING SITE FOR RESIDUE DMS A 307
08	AC8	SOFTWARE	ASN A:120 , TYR A:121 , ARG A:127 , PGO A:309 , HOH A:447	BINDING SITE FOR RESIDUE PEG A 308
09	AC9	SOFTWARE	ASN A:119 , ARG A:127 , PEG A:308	BINDING SITE FOR RESIDUE PGO A 309
10	BC1	SOFTWARE	ILE A:180 , LEU A:181 , ALA A:182 , LEU A:214 , THR A:215 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , ZN A:301 , ILE B:180 , LEU B:181 , ALA B:182 , LEU B:214 , HIS B:218 , GLU B:219 , HIS B:222 , HIS B:228 , VAL B:235 , PHE B:237 , PRO B:238 , THR B:239 , TYR B:240 , ZN B:602 , GOL B:608 , HOH B:728 , HOH B:729 , HOH B:731	BINDING SITE FOR RESIDUE L29 B 601
11	BC2	SOFTWARE	HIS B:218 , HIS B:222 , HIS B:228 , L29 B:601	BINDING SITE FOR RESIDUE ZN B 602
12	BC3	SOFTWARE	HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196	BINDING SITE FOR RESIDUE ZN B 603
13	BC4	SOFTWARE	ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:735	BINDING SITE FOR RESIDUE CA B 604
14	BC5	SOFTWARE	ASP B:124 , GLU B:199 , GLU B:201 , HOH B:708	BINDING SITE FOR RESIDUE CA B 605
15	BC6	SOFTWARE	ASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201	BINDING SITE FOR RESIDUE CA B 606
16	BC7	SOFTWARE	GLY A:178 , GLY A:179 , TYR B:240 , TYR B:242 , HOH B:750	BINDING SITE FOR RESIDUE PEG B 607
17	BC8	SOFTWARE	THR B:239 , LYS B:241 , VAL B:243 , L29 B:601 , HOH B:732	BINDING SITE FOR RESIDUE GOL B 608
18	BC9	SOFTWARE	HIS C:218 , HIS C:222 , HIS C:228 , L29 C:306	BINDING SITE FOR RESIDUE ZN C 301
19	CC1	SOFTWARE	HIS C:168 , ASP C:170 , HIS C:183 , HIS C:196	BINDING SITE FOR RESIDUE ZN C 302
20	CC2	SOFTWARE	ASP C:158 , GLY C:190 , GLY C:192 , ASP C:194 , HOH C:413	BINDING SITE FOR RESIDUE CA C 303
21	CC3	SOFTWARE	ASP C:124 , GLU C:199 , GLU C:201	BINDING SITE FOR RESIDUE CA C 304
22	CC4	SOFTWARE	ASP C:175 , GLY C:176 , GLY C:178 , ILE C:180 , ASP C:198 , GLU C:201	BINDING SITE FOR RESIDUE CA C 305
23	CC5	SOFTWARE	ILE C:180 , LEU C:181 , ALA C:182 , LEU C:214 , HIS C:218 , GLU C:219 , HIS C:222 , HIS C:228 , VAL C:235 , PHE C:237 , PRO C:238 , THR C:239 , TYR C:240 , ZN C:301 , HOH C:444 , HOH C:445 , ILE D:180 , LEU D:181 , ALA D:182 , LEU D:214 , HIS D:218 , GLU D:219 , HIS D:222 , HIS D:228 , VAL D:235 , PHE D:237 , PRO D:238 , THR D:239 , TYR D:240 , ZN D:301 , HOH D:415	BINDING SITE FOR RESIDUE L29 C 306
24	CC6	SOFTWARE	GLU B:128 , TYR C:116 , ARG C:135 , PHE C:149 , LYS C:151 , HOH C:411 , HOH C:423 , HOH C:435	BINDING SITE FOR RESIDUE PEG C 307
25	CC7	SOFTWARE	L29 C:306 , HIS D:218 , HIS D:222 , HIS D:228	BINDING SITE FOR RESIDUE ZN D 301
26	CC8	SOFTWARE	HIS D:168 , ASP D:170 , HIS D:183 , HIS D:196	BINDING SITE FOR RESIDUE ZN D 302
27	CC9	SOFTWARE	ASP D:158 , GLY D:190 , GLY D:192 , ASP D:194 , HOH D:410	BINDING SITE FOR RESIDUE CA D 303
28	DC1	SOFTWARE	ASP D:124 , GLU D:199 , GLU D:201 , HOH D:408 , HOH D:449	BINDING SITE FOR RESIDUE CA D 304
29	DC2	SOFTWARE	ASP D:175 , GLY D:176 , GLY D:178 , ILE D:180 , ASP D:198 , GLU D:201	BINDING SITE FOR RESIDUE CA D 305
30	DC3	SOFTWARE	VAL D:108 , ARG D:110 , LYS D:111 , GLY D:188	BINDING SITE FOR RESIDUE PEG D 306

(no "SS Bond" information available for 4H49)

(no "Cis Peptide Bond" information available for 4H49)

(no "SAP(SNP)/Variant" information available for 4H49)

(no "PROSITE Motif" information available for 4H49)

(no "Exon" information available for 4H49)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4h49a_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h49 A 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain B from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4h49b_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h49 B 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain C from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains d4h49c_ C: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h49 C 108 VWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

Chain D from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4h49d_ D: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...................hhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h49 D 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Superfamilies( (-)

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Families(

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Zincin-like (701)

Superfamily: Metalloproteases (zincins), catalytic domain (647)

Family: Matrix metalloproteases, catalytic domain (199)

Protein domain: automated matches (32)

Human (Homo sapiens) [TaxId: 9606] (32)

1a	d4h49a_	A:
1b	d4h49b_	B:
1c	d4h49c_	C:
1d	d4h49d_	D:

(no "CATH Domain" information available for 4H49)

(no "Pfam Domain" information available for 4H49)

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	4h49
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3lir	HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR.
4efs	HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR.
4h1q	CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR
4h2e	CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR
4h30	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A TWIN INHIBITOR.

Description

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Ligands, Modified Residues, Ions (7, 30)

Sites (30, 30)

SS Bonds (0, 0)

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