4H82 - JenaLib

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Title :   CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR.

Authors :   C. Antoni, E. A. Stura, L. Vera, E. Cassar-Lajeunesse, E. Nuti, V. Dive, A. Rossello

Date :   21 Sep 12 (Deposition) - 01 May 13 (Release) - 12 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Hydrolase/Twin Inhibitor, Zincin-Like, Gelatinase, Collagenase (Catalytic Domain), 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
(for further references see the PDB file header)

Molecule 1 - MATRIX METALLOPROTEINASE-9
	Chains	:	A, B, C, D
	EC Number	:	3.4.24.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-14B
	Expression System Strain	:	BL21 (DE3 STAR)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PT7 PROMOTER
	Fragment	:	MMP-9 CATALYTIC DOMAIN 107-215,391-444
	Gene	:	CLG4B, MMP9
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MMP-9, 92 KDA GELATINASE, 92 KDA TYPE IV COLLAGENASE, GELATINASE B, GELB, 67 KDA MATRIX METALLOPROTEINASE-9, 82 KDA MATRIX METALLOPROTEINASE-9

		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, 34)

No.	Name	Count	Type	Full Name
1	CA	12	Ligand/Ion	CALCIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	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)
4	PEG	7	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGO	3	Ligand/Ion	S-1,2-PROPANEDIOL
6	PPI	1	Ligand/Ion	PROPANOIC ACID
7	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	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)
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGO	-1	Ligand/Ion	S-1,2-PROPANEDIOL
6	PPI	-1	Ligand/Ion	PROPANOIC ACID
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (5, 13)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	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)
4	PEG	7	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGO	3	Ligand/Ion	S-1,2-PROPANEDIOL
6	PPI	1	Ligand/Ion	PROPANOIC ACID
7	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (34, 34)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:226 , HIS A:230 , HIS A:236 , L29 A:306	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	HIS A:175 , ASP A:177 , HIS A:190 , HIS A:203	BINDING SITE FOR RESIDUE ZN A 302
03	AC3	SOFTWARE	ASP A:165 , GLY A:197 , GLN A:199 , ASP A:201 , HOH A:439 , HOH A:462	BINDING SITE FOR RESIDUE CA A 303
04	AC4	SOFTWARE	ASP A:182 , GLY A:183 , ASP A:185 , LEU A:187 , ASP A:205 , GLU A:208	BINDING SITE FOR RESIDUE CA A 304
05	AC5	SOFTWARE	ASP A:131 , ASP A:206 , GLU A:208 , HOH A:428	BINDING SITE FOR RESIDUE CA A 305
06	AC6	SOFTWARE	GLY A:186 , LEU A:187 , LEU A:188 , ALA A:189 , HIS A:190 , LEU A:222 , HIS A:226 , GLN A:227 , HIS A:230 , HIS A:236 , LEU A:243 , TYR A:245 , PRO A:246 , MET A:247 , TYR A:248 , ZN A:301 , HOH A:427 , HOH A:470 , HOH A:494 , HOH A:565 , GLY B:186 , LEU B:187 , LEU B:188 , ALA B:189 , HIS B:190 , LEU B:222 , HIS B:226 , GLN B:227 , HIS B:230 , HIS B:236 , LEU B:243 , TYR B:245 , PRO B:246 , MET B:247 , ZN B:300 , HOH B:401	BINDING SITE FOR RESIDUE L29 A 306
07	AC7	SOFTWARE	L29 A:306 , HIS B:226 , HIS B:230 , HIS B:236	BINDING SITE FOR RESIDUE ZN B 300
08	AC8	SOFTWARE	HIS B:175 , ASP B:177 , HIS B:190 , HIS B:203	BINDING SITE FOR RESIDUE ZN B 301
09	AC9	SOFTWARE	ASP B:165 , GLY B:197 , GLN B:199 , ASP B:201 , HOH B:437 , HOH B:567	BINDING SITE FOR RESIDUE CA B 302
10	BC1	SOFTWARE	ASP B:182 , GLY B:183 , ASP B:185 , LEU B:187 , ASP B:205 , GLU B:208	BINDING SITE FOR RESIDUE CA B 303
11	BC2	SOFTWARE	ASP B:131 , ASP B:206 , GLU B:208 , HOH B:419	BINDING SITE FOR RESIDUE CA B 304
12	BC3	SOFTWARE	HIS C:226 , HIS C:230 , HIS C:236 , L29 D:303	BINDING SITE FOR RESIDUE ZN C 301
13	BC4	SOFTWARE	HIS C:175 , ASP C:177 , HIS C:190 , HIS C:203	BINDING SITE FOR RESIDUE ZN C 302
14	BC5	SOFTWARE	ASP C:165 , GLY C:197 , GLN C:199 , ASP C:201 , HOH C:415 , HOH C:447	BINDING SITE FOR RESIDUE CA C 303
15	BC6	SOFTWARE	ASP C:182 , GLY C:183 , ASP C:185 , LEU C:187 , ASP C:205 , GLU C:208	BINDING SITE FOR RESIDUE CA C 304
16	BC7	SOFTWARE	SER C:129 , ASP C:131 , ASP C:206 , GLU C:208 , TRP C:210	BINDING SITE FOR RESIDUE CA C 305
17	BC8	SOFTWARE	HOH C:553	BINDING SITE FOR RESIDUE PEG C 306
18	BC9	SOFTWARE	ASP C:177 , GLY C:178 , TYR C:179 , HOH C:430 , HOH C:431 , HOH C:486	BINDING SITE FOR RESIDUE PEG C 307
19	CC1	SOFTWARE	HOH C:414 , HOH C:487 , HOH C:533 , HOH C:534	BINDING SITE FOR RESIDUE PPI C 308
20	CC2	SOFTWARE	SER C:238 , VAL C:239 , PRO C:240 , HOH C:421 , HOH D:406	BINDING SITE FOR RESIDUE PEG C 309
21	CC3	SOFTWARE	LYS C:214 , ASP D:139 , PEG D:309	BINDING SITE FOR RESIDUE PEG C 310
22	CC4	SOFTWARE	HOH C:475	BINDING SITE FOR RESIDUE PEG C 311
23	CC5	SOFTWARE	LYS C:214 , PHE C:250 , HOH C:515 , HOH C:526	BINDING SITE FOR RESIDUE GOL C 312
24	CC6	SOFTWARE	HIS C:236 , SER C:237 , ASP C:259 , HOH C:405 , HOH C:506 , HOH C:507 , HOH C:508 , HOH C:509 , HOH C:533	BINDING SITE FOR RESIDUE PEG C 313
25	CC7	SOFTWARE	ASP C:185 , HOH C:453 , TYR D:248 , ARG D:249 , HOH D:409 , HOH D:546 , HOH D:558	BINDING SITE FOR RESIDUE PGO D 301
26	CC8	SOFTWARE	HIS D:175 , ASP D:177 , HIS D:190 , HIS D:203	BINDING SITE FOR RESIDUE ZN D 302
27	CC9	SOFTWARE	LEU C:187 , LEU C:188 , ALA C:189 , LEU C:222 , VAL C:223 , HIS C:226 , GLN C:227 , HIS C:230 , HIS C:236 , LEU C:243 , TYR C:245 , PRO C:246 , MET C:247 , TYR C:248 , ZN C:301 , GLY D:186 , LEU D:187 , LEU D:188 , ALA D:189 , LEU D:222 , VAL D:223 , HIS D:226 , GLN D:227 , HIS D:230 , HIS D:236 , LEU D:243 , TYR D:245 , PRO D:246 , TYR D:248 , ZN D:304 , HOH D:401 , HOH D:402 , HOH D:405	BINDING SITE FOR RESIDUE L29 D 303
28	DC1	SOFTWARE	HIS D:226 , HIS D:230 , HIS D:236 , L29 D:303	BINDING SITE FOR RESIDUE ZN D 304
29	DC2	SOFTWARE	ASP D:182 , GLY D:183 , ASP D:185 , LEU D:187 , ASP D:205 , GLU D:208	BINDING SITE FOR RESIDUE CA D 305
30	DC3	SOFTWARE	ASP D:131 , ASP D:206 , GLU D:208	BINDING SITE FOR RESIDUE CA D 306
31	DC4	SOFTWARE	ASP D:165 , GLY D:197 , GLN D:199 , ASP D:201 , HOH D:422 , HOH D:423	BINDING SITE FOR RESIDUE CA D 307
32	DC5	SOFTWARE	PHE D:221 , PRO D:254 , PRO D:255 , HOH D:433	BINDING SITE FOR RESIDUE PGO D 308
33	DC6	SOFTWARE	PEG C:310 , HOH D:520	BINDING SITE FOR RESIDUE PEG D 309
34	DC7	SOFTWARE	GLY D:215 , GLY D:217 , HOH D:474 , HOH D:558	BINDING SITE FOR RESIDUE PGO D 310

(no "SS Bond" information available for 4H82)

(no "Cis Peptide Bond" information available for 4H82)

(no "SAP(SNP)/Variant" information available for 4H82)

(no "PROSITE Motif" information available for 4H82)

(no "Exon" information available for 4H82)

Asymmetric Unit

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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains d4h82a_ A: Gelatinase B (MMP-9)                                                                                                                                  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
                 4h82 A 110 FEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269

Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains d4h82b_ B: Gelatinase B (MMP-9)                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee.......hhhhhhhhhhhhhhhhhhh...eeee.......eeeeee.................eee..........eeee....ee......eehhhhhhhhhhhh.........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h82 B 110 FEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269

Chain C from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains d4h82c_ C: Gelatinase B (MMP-9)                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee.......hhhhhhhhhhhhhhhhhhhh..eeee.......eeeeee.................eee..........eeee....ee......eehhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h82 C 110 FEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269

Chain D from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains d4h82d_ D: Gelatinase B (MMP-9)                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee......eehhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h82 D 110 FEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269

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Asymmetric Unit

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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: Gelatinase B (MMP-9) (13)

Human (Homo sapiens) [TaxId: 9606] (13)

1a	d4h82a_	A:
1b	d4h82b_	B:
1c	d4h82c_	C:
1d	d4h82d_	D:

(no "CATH Domain" information available for 4H82)

(no "Pfam Domain" information available for 4H82)

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	4h82
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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 MUTANT MMP-12 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR.
4h3x	CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A HYDROXAMATE BASED INHIBITOR.
4h49	CRYSTAL STRUCTURE OF MUTANT MMP-12 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR.
4h84

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 34)

Sites (34, 34)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (38, 38)

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