4H84 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MMP12 IN COMPLEX WITH A SELECTIVE CARBOXYLATE BASED INHIBITOR.

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

Date :   21 Sep 12 (Deposition) - 24 Apr 13 (Release) - 12 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.59

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

Keywords :   Selective Carboxylate Based Mmp-12 Inhibitor, 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
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 30)

Asymmetric Unit (7, 30)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	GOL	7	Ligand/Ion	GLYCEROL
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	7	Ligand/Ion	S-1,2-PROPANEDIOL
5	PGR	1	Ligand/Ion	R-1,2-PROPANEDIOL
6	Y38	2	Ligand/Ion	N-[2-(BENZOYLAMINO)ETHYL]-N-(BIPHENYL-4-YLSULFONYL)-D-VALINE
7	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (5, 13)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	4	Ligand/Ion	S-1,2-PROPANEDIOL
5	PGR	1	Ligand/Ion	R-1,2-PROPANEDIOL
6	Y38	1	Ligand/Ion	N-[2-(BENZOYLAMINO)ETHYL]-N-(BIPHENYL-4-YLSULFONYL)-D-VALINE
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	3	Ligand/Ion	S-1,2-PROPANEDIOL
5	PGR	-1	Ligand/Ion	R-1,2-PROPANEDIOL
6	Y38	1	Ligand/Ion	N-[2-(BENZOYLAMINO)ETHYL]-N-(BIPHENYL-4-YLSULFONYL)-D-VALINE
7	ZN	-1	Ligand/Ion	ZINC ION

Sites (30, 30)

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:218 , HIS A:222 , HIS A:228 , Y38 A:306	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:401 , HOH A:406	BINDING SITE FOR RESIDUE CA A 303
04	AC4	SOFTWARE	ASP A:124 , GLU A:199 , GLU A:201 , HOH A:402 , HOH A:471	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	ILE A:180 , LEU A:181 , ALA A:182 , LEU A:214 , 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 , PGO A:314 , HIS B:172 , HIS B:183 , ALA B:184 , PHE B:185 , HOH B:423 , HOH B:477	BINDING SITE FOR RESIDUE Y38 A 306
07	AC7	SOFTWARE	ASP A:171 , HIS A:172 , THR B:239 , TYR B:240 , Y38 B:301 , HOH B:485	BINDING SITE FOR RESIDUE PGO A 307
08	AC8	SOFTWARE	LEU A:181 , GLY A:209 , THR A:210 , TYR A:240 , HOH A:501	BINDING SITE FOR RESIDUE PGR A 308
09	AC9	SOFTWARE	GLY A:106 , PRO A:107 , ARG A:110	BINDING SITE FOR RESIDUE PGO A 309
10	BC1	SOFTWARE	PHE A:163 , ALA A:164 , ARG A:165 , SER A:189 , HOH A:419 , HOH A:427 , HOH A:430	BINDING SITE FOR RESIDUE GOL A 310
11	BC2	SOFTWARE	LYS A:111 , MET A:156 , ASP A:158 , ALA A:167 , ASP A:170 , ASP A:171 , HIS A:172 , ALA A:173 , HOH A:405 , HOH A:444 , HOH A:479	BINDING SITE FOR RESIDUE PGO A 311
12	BC3	SOFTWARE	GLY A:225 , GLY A:227 , HIS A:228 , HOH A:418 , HOH A:451 , HOH A:474 , GLY B:225 , GLY B:227	BINDING SITE FOR RESIDUE PEG A 312
13	BC4	SOFTWARE	ARG A:110 , HIS A:112 , ASP A:200 , HOH A:471 , HOH A:517	BINDING SITE FOR RESIDUE PEG A 313
14	BC5	SOFTWARE	GLY A:179 , THR A:239 , TYR A:240 , Y38 A:306 , HOH A:467 , HOH A:475 , ASP B:171 , HIS B:172	BINDING SITE FOR RESIDUE PGO A 314
15	BC6	SOFTWARE	PRO A:123 , HOH A:535	BINDING SITE FOR RESIDUE GOL A 315
16	BC7	SOFTWARE	ARG A:127 , HOH A:505 , ARG B:135	BINDING SITE FOR RESIDUE GOL A 316
17	BC8	SOFTWARE	TRP A:109 , ARG A:110 , HIS A:168 , GLY A:169 , GLY A:188 , HOH A:425 , HOH A:438	BINDING SITE FOR RESIDUE GOL A 317
18	BC9	SOFTWARE	TYR A:132 , THR A:205 , PHE A:213 , ILE A:245 , HOH A:404 , HOH A:468 , HOH A:472 , HOH A:500	BINDING SITE FOR RESIDUE PEG A 318
19	CC1	SOFTWARE	HIS A:172 , HIS A:183 , ALA A:184 , PHE A:185 , PGO A:307 , HOH A:411 , 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 , TYR B:240 , ZN B:302 , GOL B:309 , HOH B:423	BINDING SITE FOR RESIDUE Y38 B 301
20	CC2	SOFTWARE	HIS B:218 , HIS B:222 , HIS B:228 , Y38 B:301	BINDING SITE FOR RESIDUE ZN B 302
21	CC3	SOFTWARE	HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196	BINDING SITE FOR RESIDUE ZN B 303
22	CC4	SOFTWARE	ARG A:256 , ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:403	BINDING SITE FOR RESIDUE CA B 304
23	CC5	SOFTWARE	ASP B:124 , GLU B:199 , GLU B:201 , HOH B:402 , HOH B:415	BINDING SITE FOR RESIDUE CA B 305
24	CC6	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
25	CC7	SOFTWARE	ASP A:175 , ASP B:175 , LYS B:177	BINDING SITE FOR RESIDUE PGO B 307
26	CC8	SOFTWARE	TYR B:132 , ALA B:133 , LYS B:136 , THR B:205 , ILE B:245 , HOH B:406 , HOH B:413	BINDING SITE FOR RESIDUE PGO B 308
27	CC9	SOFTWARE	LYS B:233 , ALA B:234 , THR B:239 , LYS B:241 , Y38 B:301 , HOH B:480	BINDING SITE FOR RESIDUE GOL B 309
28	DC1	SOFTWARE	VAL B:108 , TRP B:109 , ARG B:110 , GLY B:188 , HOH B:527	BINDING SITE FOR RESIDUE GOL B 310
29	DC2	SOFTWARE	LYS A:233 , PRO B:146 , TYR B:262	BINDING SITE FOR RESIDUE GOL B 311
30	DC3	SOFTWARE	LYS B:136 , ILE B:245 , HOH B:463	BINDING SITE FOR RESIDUE PGO B 312

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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:159
                                                                                                                                                                                               
               SCOP domains d4h84a_ A: automated matches                                                                                                                                    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
                 4h84 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 d4h84b_ B: 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
                 4h84 B 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (21, 21)

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	4h84
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