4H2E - JenaLib

Title :   CRYSTAL STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9 CATALYTIC DOMAINS

Authors :   E. A. Stura, L. Vera, E. Cassar-Lajeunesse, E. Nuti, M. P. Catalani, V. D A. Rossello

Date :   12 Sep 12 (Deposition) - 24 Apr 13 (Release) - 31 May 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 26)

Asymmetric Unit (6, 26)

No.	Name	Count	Type	Full Name
1	0Y3	1	Ligand/Ion	N,N'-BIS(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE
2	ACT	4	Ligand/Ion	ACETATE ION
3	BCN	3	Ligand/Ion	BICINE
4	CA	5	Ligand/Ion	CALCIUM ION
5	PEG	9	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 11)

No.	Name	Count	Type	Full Name
1	0Y3	-1	Ligand/Ion	N,N'-BIS(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE
2	ACT	3	Ligand/Ion	ACETATE ION
3	BCN	2	Ligand/Ion	BICINE
4	CA	-1	Ligand/Ion	CALCIUM ION
5	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	0Y3	1	Ligand/Ion	N,N'-BIS(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE
2	ACT	1	Ligand/Ion	ACETATE ION
3	BCN	1	Ligand/Ion	BICINE
4	CA	-1	Ligand/Ion	CALCIUM ION
5	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	ZN	-1	Ligand/Ion	ZINC ION

Sites (26, 26)

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:226 , HIS A:230 , HIS A:236 , 0Y3 B: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	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	LYS A:258 , ALA B:146	BINDING SITE FOR RESIDUE PEG A 305
06	AC6	SOFTWARE	GLU A:241 , HOH A:425 , PEG B:308 , HOH B:460	BINDING SITE FOR RESIDUE PEG A 306
07	AC7	SOFTWARE	PEG A:308	BINDING SITE FOR RESIDUE PEG A 307
08	AC8	SOFTWARE	TYR A:179 , PEG A:307 , HOH A:420	BINDING SITE FOR RESIDUE PEG A 308
09	AC9	SOFTWARE	ALA A:173 , GLU A:174 , PHE A:181 , ACT A:312 , BCN A:314	BINDING SITE FOR RESIDUE PEG A 309
10	BC1	SOFTWARE	ASN A:127 , VAL A:172	BINDING SITE FOR RESIDUE PEG A 310
11	BC2	SOFTWARE	HOH A:440	BINDING SITE FOR RESIDUE ACT A 311
12	BC3	SOFTWARE	PEG A:309	BINDING SITE FOR RESIDUE ACT A 312
13	BC4	SOFTWARE	HOH A:463	BINDING SITE FOR RESIDUE ACT A 313
14	BC5	SOFTWARE	ASP A:182 , PEG A:309 , ARG B:249 , GLU B:252	BINDING SITE FOR RESIDUE BCN A 314
15	BC6	SOFTWARE	HOH A:473	BINDING SITE FOR RESIDUE BCN A 315
16	BC7	SOFTWARE	HIS B:226 , HIS B:230 , HIS B:236 , 0Y3 B:306	BINDING SITE FOR RESIDUE ZN B 301
17	BC8	SOFTWARE	HIS B:175 , ASP B:177 , HIS B:190 , HIS B:203	BINDING SITE FOR RESIDUE ZN B 302
18	BC9	SOFTWARE	ALA B:164 , ASP B:165 , GLY B:197 , GLN B:199 , ASP B:201	BINDING SITE FOR RESIDUE CA B 303
19	CC1	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 304
20	CC2	SOFTWARE	SER B:129 , ASP B:131 , ASP B:206 , GLU B:208 , TRP B:210	BINDING SITE FOR RESIDUE CA B 305
21	CC3	SOFTWARE	LEU A:187 , LEU A:188 , ALA A:189 , LEU A:222 , HIS A:226 , GLU A:227 , HIS A:230 , ASP A:235 , HIS A:236 , LEU A:243 , TYR A:245 , PRO A:246 , TYR A:248 , ZN A:301 , GLY B:106 , PHE B:107 , LEU B:188 , ALA B:189 , LEU B:222 , VAL B:223 , HIS B:226 , GLU B:227 , HIS B:230 , ASP B:235 , HIS B:236 , LEU B:243 , TYR B:245 , PRO B:246 , MET B:247 , TYR B:248 , ZN B:301 , HOH B:437 , HOH B:459	BINDING SITE FOR RESIDUE 0Y3 B 306
22	CC4	SOFTWARE	PEG B:308	BINDING SITE FOR RESIDUE PEG B 307
23	CC5	SOFTWARE	PEG A:306 , PRO B:180 , PEG B:307 , PEG B:309	BINDING SITE FOR RESIDUE PEG B 308
24	CC6	SOFTWARE	GLY B:178 , TYR B:179 , PEG B:308	BINDING SITE FOR RESIDUE PEG B 309
25	CC7	SOFTWARE	PHE B:250 , THR B:251 , GLU B:252 , HOH B:458	BINDING SITE FOR RESIDUE ACT B 310
26	CC8	SOFTWARE	ALA B:173 , GLU B:174 , PRO B:180 , PHE B:181 , HOH B:449 , HOH B:457	BINDING SITE FOR RESIDUE BCN B 311

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	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:164
                                                                                                                                                                                                    
               SCOP domains d4h2ea_ A: Gelatinase B (MMP-9)                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhhhh..eeee.......eeeeee.................eee..........eeee....ee......eehhhhhhhhhhhhh........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2e A 106 GFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265

Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains d4h2eb_ B: 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........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2e B 106 GFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (38, 38)

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:253 - Pro A:254	[ RasMol ]
		Tyr B:268 - Gly B:269	[ RasMol ]

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