5I4O - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A SELECTIVE SUGAR-CONJUGATED TRIAZOLE-LINKED CARBOXYLATE ZINC-CHELATOR WATER-SOLUBLE INHIBITOR (DC28).

Authors :   E. A. Stura, L. Rosalia, D. Cuffaro, L. Tepshi, L. Ciccone, A. Rossello

Date :   12 Feb 16 (Deposition) - 06 Jul 16 (Release) - 17 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Inhibitor, Complex, Glycoconjugate, Metalloprotease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Nuti, D. Cuffaro, F. D'Andrea, L. Rosalia, L. Tepshi, M. Fabbi, G. Carbotti, S. Ferrini, S. Santamaria, C. Camodeca, L. Ciccone, E. Orlandini, S. Nencetti, E. A. Stura, V. Dive, A. Rossello
Sugar-Based Arylsulfonamide Carboxylates As Selective And Water-Soluble Matrix Metalloproteinase-12 Inhibitors.
Chemmedchem V. 11 1626 2016
PubMed-ID: 27356908 | Reference-DOI: 10.1002/CMDC.201600235

Molecule 1 - MACROPHAGE METALLOELASTASE
	Cell	:	MACROPHAGE
	Chains	:	A, B, C, D
	EC Number	:	3.4.24.65
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	STAR
	Fragment	:	UNP RESIDUES 106-238
	Gene	:	MMP12, HME
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CATALYTIC DOMAIN OF HUMAN MACROPHAGE ELASTASE (MMP-12)
	Synonym	:	MME,MACROPHAGE ELASTASE,HME,MATRIX METALLOPROTEINASE-12,MMP- 12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 24)

No.	Name	Count	Type	Full Name
1	CA	12	Ligand/Ion	CALCIUM ION
2	V28	4	Ligand/Ion	N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-D-VALINE
3	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	V28	1	Ligand/Ion	N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-D-VALINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	V28	1	Ligand/Ion	N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-D-VALINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	V28	1	Ligand/Ion	N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-D-VALINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	V28	1	Ligand/Ion	N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-D-VALINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , HIS A:183 , LEU A:214 , HIS A:218 , GLN A:219 , HIS A:222 , HIS A:228 , VAL A:235 , PHE A:237 , PRO A:238 , TYR A:240 , ZN A:302 , HOH A:603 , GLU C:128 , ARG C:135	binding site for residue V28 A 301
02	AC2	SOFTWARE	HIS A:218 , HIS A:222 , HIS A:228 , V28 A:301	binding site for residue ZN A 302
03	AC3	SOFTWARE	HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196	binding site for residue ZN A 303
04	AC4	SOFTWARE	ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:615 , HOH A:616	binding site for residue CA A 304
05	AC5	SOFTWARE	ASP A:124 , GLU A:199 , GLU A:201 , HOH A:655 , HOH A:676	binding site for residue CA A 305
06	AC6	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 306
07	AC7	SOFTWARE	GLY B:179 , ILE B:180 , LEU B:181 , ALA B:182 , HIS B:183 , LEU B:214 , HIS B:218 , GLN 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:302 , LYS D:241	binding site for residue V28 B 301
08	AC8	SOFTWARE	HIS B:218 , HIS B:222 , HIS B:228 , V28 B:301	binding site for residue ZN B 302
09	AC9	SOFTWARE	HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196 , HOH B:603	binding site for residue ZN B 303
10	AD1	SOFTWARE	ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:624	binding site for residue CA B 304
11	AD2	SOFTWARE	HOH A:627 , HOH A:698 , ASP B:124 , GLU B:199 , GLU B:201	binding site for residue CA B 305
12	AD3	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 306
13	AD4	SOFTWARE	GLU A:128 , GLY C:179 , ILE C:180 , LEU C:181 , ALA C:182 , LEU C:214 , HIS C:218 , GLN C:219 , HIS C:222 , HIS C:228 , VAL C:235 , PHE C:237 , PRO C:238 , TYR C:240 , ZN C:302 , HOH C:601 , HOH C:650	binding site for residue V28 C 301
14	AD5	SOFTWARE	HIS C:218 , HIS C:222 , HIS C:228 , V28 C:301	binding site for residue ZN C 302
15	AD6	SOFTWARE	HIS C:168 , ASP C:170 , HIS C:183 , HIS C:196	binding site for residue ZN C 303
16	AD7	SOFTWARE	ASP C:158 , GLY C:190 , GLY C:192 , ASP C:194 , HOH C:618 , HOH C:627	binding site for residue CA C 304
17	AD8	SOFTWARE	ASP C:124 , GLU C:199 , GLU C:201 , HOH C:671 , HOH C:677	binding site for residue CA C 305
18	AD9	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 306
19	AE1	SOFTWARE	LYS B:233 , HOH B:622 , ILE D:180 , LEU D:181 , ALA D:182 , HIS D:183 , LEU D:214 , HIS D:218 , GLN D:219 , HIS D:222 , HIS D:228 , VAL D:235 , PHE D:237 , PRO D:238 , THR D:239 , TYR D:240 , LYS D:241 , ZN D:302 , HOH D:609	binding site for residue V28 D 301
20	AE2	SOFTWARE	HIS D:218 , HIS D:222 , HIS D:228 , V28 D:301	binding site for residue ZN D 302
21	AE3	SOFTWARE	HIS D:168 , ASP D:170 , HIS D:183 , HIS D:196	binding site for residue ZN D 303
22	AE4	SOFTWARE	ASP D:158 , GLY D:190 , GLY D:192 , ASP D:194 , HOH D:606	binding site for residue CA D 304
23	AE5	SOFTWARE	ASP D:124 , GLU D:199 , GLU D:201 , HOH D:640	binding site for residue CA D 305
24	AE6	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 306

(no "SS Bond" information available for 5I4O)

Asymmetric Unit

No.	Residues
1	Tyr D:262	-	Gly D:263

(no "SAP(SNP)/Variant" information available for 5I4O)

(no "PROSITE Motif" information available for 5I4O)

(no "Exon" information available for 5I4O)

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:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...................hhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i4o A 108 VWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

Chain B from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i4o B 108 VWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

Chain C from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh..................hhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i4o C 108 VWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

Chain D from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ 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
                 5i4o D 108 VWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

Legend:		→ Mismatch	(orange background)
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	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 '\|'

(no "SCOP Domain" information available for 5I4O)

(no "CATH Domain" information available for 5I4O)

(no "Pfam Domain" information available for 5I4O)

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Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Tyr D:262 - Gly D:263	[ RasMol ]

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	5i4o
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5i12	MMP-9 COMPLEXED WITH RELATED INHIBITOR
5i2z	SAME PROTEIN COMPLEXED WITH RELATED INHIBITOR
5i3m	SAME PROTEIN COMPLEXED WITH RELATED INHIBITOR
5i43	SAME PROTEIN COMPLEXED WITH RELATED INHIBITOR
5iol	SAME PROTEIN COMPLEXED WITH RELATED INHIBITOR

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 24)

Sites (24, 24)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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