3V96 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   COMPLEX OF MATRIX METALLOPROTEINASE-10 CATALYTIC DOMAIN (MMP-10CD) WITH TISSUE INHIBITOR OF METALLOPROTEINASES-1 (TIMP-1)

Authors :   J. Batra, A. S. Soares, E. S. Radisky

Date :   23 Dec 11 (Deposition) - 28 Mar 12 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Metzincin, Ob-Fold, Metalloproteinase, Protease Inhibitor, Hydrolase Inhibitor-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Batra, J. Robinson, A. S. Soares, A. P. Fields, D. C. Radisky, E. S. Radisky
Matrix Metalloproteinase-10 (Mmp-10) Interaction With Tissu Inhibitors Of Metalloproteinases Timp-1 And Timp-2: Binding Studies And Crystal Structure.
J. Biol. Chem. V. 287 15935 2012
PubMed-ID: 22427646 | Reference-DOI: 10.1074/JBC.M112.341156

Molecule 1 - METALLOPROTEINASE INHIBITOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293E
	Expression System Plasmid	:	PTT/TIMP1
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 24-207
	Gene	:	CLGI, TIMP, TIMP1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ERYTHROID-POTENTIATING ACTIVITY, EPA, FIBROBLAST COLLAGENASE INHIBITOR, COLLAGENASE INHIBITOR, TISSUE INHIBITOR OF METALLOPROTEINASES 1, TIMP-1

Molecule 2 - STROMELYSIN-2
	Chains	:	B
	EC Number	:	3.4.24.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MMP-10CDNA
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 99-263
	Gene	:	MMP10, STMY2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SL-2, MATRIX METALLOPROTEINASE-10, MMP-10, TRANSIN-2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:59 , ARG A:162 , HIS A:163 , HOH A:351 , HOH A:371	BINDING SITE FOR RESIDUE PO4 A 201
2	AC2	SOFTWARE	SER A:100 , VAL A:102 , GLU A:156 , LYS A:157 , HOH A:370	BINDING SITE FOR RESIDUE PO4 A 202
3	AC3	SOFTWARE	CYS A:1 , HIS B:217 , HIS B:221 , HIS B:227	BINDING SITE FOR RESIDUE ZN B 301
4	AC4	SOFTWARE	HIS B:167 , ASP B:169 , HIS B:182 , HIS B:195	BINDING SITE FOR RESIDUE ZN B 302
5	AC5	SOFTWARE	ASP B:174 , GLY B:175 , GLY B:177 , SER B:179 , ASP B:197 , GLU B:200	BINDING SITE FOR RESIDUE CA B 303
6	AC6	SOFTWARE	ASP B:157 , GLY B:189 , TYR B:191 , ASP B:193 , HOH B:447 , HOH B:449	BINDING SITE FOR RESIDUE CA B 304
7	AC7	SOFTWARE	ASP B:123 , ASP B:198 , GLU B:200	BINDING SITE FOR RESIDUE CA B 305

Asymmetric/Biological Unit

No.	Residues
1	A:1	-	A:70
2	A:3	-	A:99
3	A:13	-	A:124
4	A:127	-	A:174
5	A:132	-	A:137
6	A:145	-	A:166

(no "Cis Peptide Bond" information available for 3V96)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036139	E	142	Q	MMP10_HUMAN	Unclassified	---	B	E	142	Q
2	CancerSNP	VAR_MMP10_HUMAN_CCDS8321_1_01 *	E	142	Q	MMP10_HUMAN	Disease (Breast cancer)	---	B	E	142	Q
3	UniProt	VAR_020952	F	226	L	MMP10_HUMAN	Polymorphism	17860971	B	F	226	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NTR	PS50189	NTR domain profile.	TIMP1_HUMAN	24-147	1	A:1-124
2	TIMP	PS00288	Tissue inhibitors of metalloproteinases signature.	TIMP1_HUMAN	24-36	1	A:1-13
3	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP10_HUMAN	214-223	1	B:214-223

Asymmetric/Biological Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000218388	1a	ENSE00001472535	X:47441712-47441873	162	TIMP1_HUMAN	-	0	0	-	-
1.3	ENST00000218388	3	ENSE00002188016	X:47442807-47442935	129	TIMP1_HUMAN	1-41	41	1	A:1-18	18
1.4a	ENST00000218388	4a	ENSE00001687541	X:47444335-47444414	80	TIMP1_HUMAN	41-67	27	1	A:18-44 (gaps)	27
1.4d	ENST00000218388	4d	ENSE00002194942	X:47444604-47444730	127	TIMP1_HUMAN	68-110	43	1	A:45-87 (gaps)	43
1.4g	ENST00000218388	4g	ENSE00001622276	X:47444942-47445066	125	TIMP1_HUMAN	110-151	42	1	A:87-128	42
1.5b	ENST00000218388	5b	ENSE00001472498	X:47445920-47446188	269	TIMP1_HUMAN	152-207	56	1	A:129-178	50

2.1	ENST00000279441	1	ENSE00000993214	chr11:102651359-102651218	142	MMP10_HUMAN	1-35	35	0	-	-
2.2	ENST00000279441	2	ENSE00000993200	chr11:102650476-102650235	242	MMP10_HUMAN	36-116	81	1	B:105-116	12
2.3	ENST00000279441	3	ENSE00001758252	chr11:102650092-102649944	149	MMP10_HUMAN	116-166	51	1	B:116-166	51
2.4	ENST00000279441	4	ENSE00000993192	chr11:102649480-102649355	126	MMP10_HUMAN	166-208	43	1	B:166-208	43
2.5	ENST00000279441	5	ENSE00001706030	chr11:102647507-102647343	165	MMP10_HUMAN	208-263	56	1	B:208-263	56
2.6	ENST00000279441	6	ENSE00000993219	chr11:102647155-102647011	145	MMP10_HUMAN	263-311	49	1	B:263-263	1
2.7	ENST00000279441	7	ENSE00000993209	chr11:102646052-102645919	134	MMP10_HUMAN	311-356	46	0	-	-
2.8	ENST00000279441	8	ENSE00001692235	chr11:102643737-102643578	160	MMP10_HUMAN	356-409	54	0	-	-
2.9	ENST00000279441	9	ENSE00000993181	chr11:102642846-102642743	104	MMP10_HUMAN	409-444	36	0	-	-
2.10	ENST00000279441	10	ENSE00000993208	chr11:102641624-102641245	380	MMP10_HUMAN	444-476	33	0	-	-

Asymmetric/Biological 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
 aligned with TIMP1_HUMAN | P01033 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:178
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193        
          TIMP1_HUMAN    24 CTCVPPHPQTAFCNSDLVIRAKFVGTPEVNQTTLYQRYEIKMTKMYKGFQALGDAADIRFVYTPAMESVCGYFHRSHNRSEEFLIAGKLQDGLLHITTCSFVAPWNSLSLAQRRGFTKTYTVGCEECTVFPCLSIPCKLQSGTHCLWTDQLLQGSEKGFQSRHLACLPREPGLCTWQS 201
               SCOP domains d3v96a_ A: TIMP-1                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhhh.eeeeeee.------....eeeeeeeeeeeee..--------..eeeee.hhhhh...........eeeeeeeee..eee......eee.hhhhhhhhhhhhhhhhhh....eeee............eeeehhhhhhh...hhhhhhheeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NTR  PDB: A:1-124 UniProt: 24-147                                                                                           ------------------------------------------------------ PROSITE (1)
                PROSITE (2) TIMP         --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3          --------------------------Exon 1.4d  PDB: A:45-87 (gaps)             -----------------------------------------Exon 1.5b  PDB: A:129-178 UniProt: 152-207         Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.4a UniProt: 41-67   ------------------------------------------Exon 1.4g  PDB: A:87-128 UniProt: 110-151 -------------------------------------------------- Transcript 1 (2)
                 3v96 A   1 CTCVPPHPQTAFCNSDLVIRAKFV------QTTLYQRYEIKMTKMYKGF--------IRFVYTPAMESVCGYFHRSHNRSEEFLIAGKLQDGLLHITTCSFVAPWNSLSLAQRRGFTKTYTVGCEECTVFPCLSIPCKLQSGTHCLWTDQLLQGSEKGFQSRHLACLPREPGLCTWQS 178
                                    10        20   |     -|       40        |-       |60        70        80        90       100       110       120       130       140       150       160       170        
                                                  24     31                49       58

Chain B from PDB  Type:PROTEIN  Length:159
 aligned with MMP10_HUMAN | P09238 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:159
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
          MMP10_HUMAN   105 MPKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDFYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNSFTELAQFRLSQDDVNGIQSLYG 263
               SCOP domains d3v96b_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee...............eeeee..........eeee....ee.....eehhhhhhhhhhhhhh................hhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------Q-----------------------------------------------------------------------------------L------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------Q------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.2    -------------------------------------------------Exon 2.4  PDB: B:166-208 UniProt: 166-208  ------------------------------------------------------2 Transcript 2 (1)
           Transcript 2 (2) -----------Exon 2.3  PDB: B:116-166 UniProt: 116-166          -----------------------------------------Exon 2.5  PDB: B:208-263 UniProt: 208-263                Transcript 2 (2)
                 3v96 B 105 MPKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDFYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNSFTELAQFRLSQDDVNGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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 '\|'

(no "CATH Domain" information available for 3V96)

(no "Pfam Domain" information available for 3V96)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TIMP1_HUMAN | P01033)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008191	metalloendopeptidase inhibitor activity	Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0051216	cartilage development	The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0001775	cell activation	A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0043086	negative regulation of catalytic activity	Any process that stops or reduces the activity of an enzyme.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0051045	negative regulation of membrane protein ectodomain proteolysis	Any process that stops, prevents, or reduces the frequency, rate or extent of membrane protein ectodomain proteolysis.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:1901164	negative regulation of trophoblast cell migration	Any process that stops, prevents or reduces the frequency, rate or extent of trophoblast cell migration.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:2001044	regulation of integrin-mediated signaling pathway	Any process that modulates the frequency, rate or extent of integrin-mediated signaling pathway.
	GO:0034097	response to cytokine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	GO:0009725	response to hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
	GO:0010033	response to organic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0043434	response to peptide hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0005604	basement membrane	A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Chain B (MMP10_HUMAN | P09238)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
cellular component
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3v96)

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	3v96
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	MMP10_HUMAN \| P09238
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	TIMP1_HUMAN \| P01033
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	3.4.24.22
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	MMP10_HUMAN \| P09238
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UniProtKB/Swiss-Prot
	MMP10_HUMAN \| P09238	:	1q3a 4ilw
	TIMP1_HUMAN \| P01033	:	1d2b 1lqn 1oo9 1uea 2j0t 3ma2

(no "Related Entries Specified in the PDB File" available for 3V96)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (3, 3)

Exons (10, 10)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (43, 49)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File