5L7F - JenaLib

Title :   CRYSTAL STRUCTURE OF MMP12 MUTANT K421A IN COMPLEX WITH RXP470.1 CONJUGATED WITH FLUOROPHORE CY5,5 IN SPACE GROUP P21.

Authors :   L. Tepshi, T. Bordenave, C. Rouanet-Mehouas, L. Devel, V. Dive, E. A. St

Date :   03 Jun 16 (Deposition) - 14 Sep 16 (Release) - 26 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Probes For Optical Imaging, Mmp-12, Metalloprotease, Inflammation, Aneurysm, Fluorophore, Cy5, 5, Cyanine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Bordenave, M. Helle, F. Beau, D. Georgiadis, L. Tepshi, M. Bernes, Y. Ye, L. Levenez, E. Poquet, H. Nozach, M. Razavian, J. Toczek, E. A. Stura, V. Dive, M. M. Sadeghi, L. Devel
Synthesis And In Vitro And In Vivo Evaluation Of Mmp-12 Selective Optical Probes.
Bioconjug. Chem. V. 27 2407 2016
PubMed-ID: 27564088 | Reference-DOI: 10.1021/ACS.BIOCONJCHEM.6B00377

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 20)

Asymmetric Unit (8, 20)

No.	Name	Count	Type	Full Name
1	6PJ	2	Ligand/Ion	CY5.5-PEG2
2	BR	1	Ligand/Ion	BROMIDE ION
3	CA	6	Ligand/Ion	CALCIUM ION
4	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
5	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
6	GOL	1	Ligand/Ion	GLYCEROL
7	R47	2	Ligand/Ion	N-[(2S)-3-[(S)-(4-BROMOPHENYL)(HYDROXY)PHOSPHORYL]-2-{[3-(3'-CHLOROBIPHENYL-4-YL)-1,2-OXAZOL-5-YL]METHYL}PROPANOYL]-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMINE
8	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	6PJ	1	Ligand/Ion	CY5.5-PEG2
2	BR	-1	Ligand/Ion	BROMIDE ION
3	CA	-1	Ligand/Ion	CALCIUM ION
4	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
5	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
6	GOL	-1	Ligand/Ion	GLYCEROL
7	R47	1	Ligand/Ion	N-[(2S)-3-[(S)-(4-BROMOPHENYL)(HYDROXY)PHOSPHORYL]-2-{[3-(3'-CHLOROBIPHENYL-4-YL)-1,2-OXAZOL-5-YL]METHYL}PROPANOYL]-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMINE
8	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (5, 5)

No.	Name	Count	Type	Full Name
1	6PJ	1	Ligand/Ion	CY5.5-PEG2
2	BR	-1	Ligand/Ion	BROMIDE ION
3	CA	-1	Ligand/Ion	CALCIUM ION
4	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
5	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
6	GOL	1	Ligand/Ion	GLYCEROL
7	R47	1	Ligand/Ion	N-[(2S)-3-[(S)-(4-BROMOPHENYL)(HYDROXY)PHOSPHORYL]-2-{[3-(3'-CHLOROBIPHENYL-4-YL)-1,2-OXAZOL-5-YL]METHYL}PROPANOYL]-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMINE
8	ZN	-1	Ligand/Ion	ZINC ION

Sites (17, 17)

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:218 , HIS A:222 , HIS A:228 , R47 A:310	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:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201	binding site for residue CA A 303
04	AC4	SOFTWARE	ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:438 , HOH A:447	binding site for residue CA A 304
05	AC5	SOFTWARE	ASP A:124 , GLU A:199 , GLU A:201 , HOH A:532 , HOH A:533	binding site for residue CA A 305
06	AC6	SOFTWARE	GLY A:209 , THR A:210 , R47 A:310	binding site for residue EDO A 308
07	AC7	SOFTWARE	PRO A:123 , MET A:125 , ASN A:126	binding site for residue EDO A 309
08	AC8	SOFTWARE	HIS B:218 , HIS B:222 , HIS B:228 , R47 B:306	binding site for residue ZN B 301
09	AC9	SOFTWARE	HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196	binding site for residue ZN B 302
10	AD1	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 303
11	AD2	SOFTWARE	ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:428 , HOH B:447	binding site for residue CA B 304
12	AD3	SOFTWARE	ASP B:124 , GLU B:199 , GLU B:201 , HOH B:530 , HOH B:540	binding site for residue CA B 305
13	AD4	SOFTWARE	SER A:229 , SER B:229 , SER B:230	binding site for residue EDO B 307
14	AD5	SOFTWARE	LEU B:181 , GLY B:209 , THR B:210 , TYR B:240 , R47 B:306	binding site for residue GOL B 308
15	AD6	SOFTWARE	HIS B:183 , ALA B:184 , PHE B:185 , R47 B:306	binding site for residue DMS B 310
16	AD7	SOFTWARE	SER A:230 , PRO A:232 , LYS A:233 , TYR A:242 , VAL A:243 , ARG A:249 , SER A:251 , ALA A:252 , HOH A:401 , HOH A:407 , HOH A:416 , HOH A:424 , HOH A:453 , HOH A:456 , HOH A:477 , ARG B:110 , LYS B:111 , GLY B:178 , GLY B:179 , ILE B:180 , LEU B:181 , ALA B:182 , THR B:215 , HIS B:218 , GLU B:219 , HIS B:222 , HIS B:228 , PRO B:232 , LYS B:233 , ALA B:234 , VAL B:235 , PHE B:237 , PRO B:238 , THR B:239 , TYR B:240 , ALA B:241 , VAL B:243 , ZN B:301 , GOL B:308 , DMS B:310 , HOH B:441 , HOH B:461 , HOH B:469 , HOH B:506	binding site for residues 6PJ A 306 and R47 B 306
17	AD8	SOFTWARE	VAL A:108 , TRP A:109 , ARG A:110 , PRO A:123 , MET A:125 , ASN A:126 , GLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , PRO A:187 , GLY A:188 , SER A:189 , THR A:215 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , PRO A:232 , LYS A:233 , ALA A:234 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , ALA A:241 , VAL A:243 , ZN A:301 , EDO A:308 , HOH A:413 , HOH A:415 , HOH A:458 , HOH A:461 , HOH A:499 , HOH A:519 , HOH A:524 , HIS B:183 , ALA B:184 , PHE B:185 , SER B:230 , PRO B:232 , LYS B:233 , THR B:247 , PHE B:248 , ARG B:249 , SER B:251 , ALA B:252 , R47 B:306 , HOH B:403 , HOH B:404 , HOH B:420 , HOH B:449 , HOH B:475 , HOH B:491	binding site for residues R47 A 310 and 6PJ B 309

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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l7f A 106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYAYVDINTFRLSADDIRGIQSLYG 263
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l7f B 106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYAYVDINTFRLSADDIRGIQSLYG 263
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (21, 21)

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