1O5B - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   DISSECTING AND DESIGNING INHIBITOR SELECTIVITY DETERMINANTS AT THE S1 SITE USING AN ARTIFICIAL ALA190 PROTEASE (ALA190 UPA)

Authors :   B. A. Katz, C. Luong, J. D. Ho, J. R. Somoza, E. Gjerstad, J. Tang, S. R. Williams, E. Verner, R. L. Mackman, W. B. Young, P. A. Sprengeler, H. Chan, K. Mortara, J. W. Janc, M. E. Mcgrath

Date :   09 Sep 03 (Deposition) - 21 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Ala190 Upa, S1 Site, Selectivity, Conserved Water Displacement Hydrogen Bond Deficit, Trypsin, Thrombin, Hepsin, Factor Viia, Blood Clotting, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Katz, C. Luong, J. D. Ho, J. R. Somoza, E. Gjerstad, J. Tang, S. R. Williams, E. Verner, R. L. Mackman, W. B. Young, P. A. Sprengeler, H. Chan, K. Mortara, J. W. Janc, M. E. Mcgrath
Dissecting And Designing Inhibitor Selectivity Determinants At The S1 Site Using An Artificial Ala190 Protease (Ala190 Upa)
J. Mol. Biol. V. 344 527 2004
PubMed-ID: 15522303 | Reference-DOI: 10.1016/J.JMB.2004.09.032
(for further references see the PDB file header)

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
	Chains	:	A
	EC Number	:	3.4.21.73
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPIC9LMWUPA-ALA190
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	SHORT CHAIN
	Gene	:	PLAU
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UPA, U-PLASMINOGEN ACTIVATOR

Molecule 2 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
	Chains	:	B
	EC Number	:	3.4.21.73
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPIC9LMWUPA-ALA190
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	PLAU
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UPA, U-PLASMINOGEN ACTIVATOR

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CIT	3	Ligand/Ion	CITRIC ACID
2	ESI	1	Ligand/Ion	4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CIT B:3 , ASP B:189 , ALA B:190 , GLN B:192 , SER B:195 , TRP B:215 , GLY B:216 , GLY B:219 , GLY B:226 , HOH B:405	BINDING SITE FOR RESIDUE ESI B 251
2	AC2	SOFTWARE	CIT B:2 , TYR B:67 , LYS B:82 , SER B:164 , HIS B:165 , ARG B:166 , HOH B:264 , HOH B:350 , HOH B:443	BINDING SITE FOR RESIDUE CIT B 1
3	AC3	SOFTWARE	CIT B:1 , ARG B:36 , LYS B:82 , LYS B:110A , HIS B:165 , ARG B:166 , ARG B:230 , HOH B:415	BINDING SITE FOR RESIDUE CIT B 2
4	AC4	SOFTWARE	HIS B:57 , GLN B:185B , GLN B:192 , GLY B:193 , SER B:195 , ESI B:251 , HOH B:354 , HOH B:407 , HOH B:464 , HOH B:465 , HOH B:466	BINDING SITE FOR RESIDUE CIT B 3

Asymmetric/Biological Unit

No.	Residues
1	A:13	-	B:122
2	B:42	-	B:58
3	B:50	-	B:111
4	B:136	-	B:201
5	B:168	-	B:182
6	B:191	-	B:220

(no "Cis Peptide Bond" information available for 1O5B)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013102	I	214	M	UROK_HUMAN	Polymorphism	---	B	M	47	M
2	UniProt	VAR_038731	K	231	Q	UROK_HUMAN	Polymorphism	2227567	B	K	61	Q

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	UROK_HUMAN	179-424	1	B:16-242
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	UROK_HUMAN	220-225	1	B:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	UROK_HUMAN	370-381	1	B:189-200

Asymmetric/Biological Unit (5, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3c	ENST00000372764	3c	ENSE00001820360	chr10:75670915-75670976	62	UROK_HUMAN	-	0	0	-	-
1.4b	ENST00000372764	4b	ENSE00002193721	chr10:75671283-75671370	88	UROK_HUMAN	1-19	19	0	-	-
1.5	ENST00000372764	5	ENSE00001276413	chr10:75671799-75671826	28	UROK_HUMAN	20-29	10	0	-	-
1.6a	ENST00000372764	6a	ENSE00001169210	chr10:75671973-75672080	108	UROK_HUMAN	29-65	37	0	-	-
1.7b	ENST00000372764	7b	ENSE00001169200	chr10:75672682-75672856	175	UROK_HUMAN	65-123	59	0	-	-
1.8	ENST00000372764	8	ENSE00000834105	chr10:75673048-75673139	92	UROK_HUMAN	123-154	32	0	-	-
1.9b	ENST00000372764	9b	ENSE00001169184	chr10:75673297-75673516	220	UROK_HUMAN	154-227	74	2	A:9-16 B:16-60	8 49
1.10	ENST00000372764	10	ENSE00001169178	chr10:75673738-75673886	149	UROK_HUMAN	227-277	51	1	- B:60-104	- 51
1.11	ENST00000372764	11	ENSE00001169173	chr10:75674534-75674674	141	UROK_HUMAN	277-324	48	1	- B:104-147	- 48
1.13	ENST00000372764	13	ENSE00001169164	chr10:75675009-75675157	149	UROK_HUMAN	324-373	50	1	- B:147-192	- 50
1.14d	ENST00000372764	14d	ENSE00001892698	chr10:75676147-75677255	1109	UROK_HUMAN	374-431	58	1	- B:193-242 (gaps)	- 51

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
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Chain A from PDB  Type:PROTEIN  Length:8
 aligned with UROK_HUMAN | P00749 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:8
          UROK_HUMAN    164 LKFQCGQK  171
               SCOP domains d1o5b.1  SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                PROSITE (1) -------- PROSITE (1)
                PROSITE (2) -------- PROSITE (2)
           Transcript 1 (1) -------- Transcript 1 (1)
           Transcript 1 (2) 1.9b     Transcript 1 (2)
                1o5b A    9 LKFQCGQK   16

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with UROK_HUMAN | P00749 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:245
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418     
          UROK_HUMAN    179 IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICLPSMYNDPQFGTSCEITGFGKENSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHT  423
               SCOP domains d1o5b.1 A:,B: Urokinase-type plasminogen activator (LMW U-PA), catalytic domain                                                                                                                                                                       SCOP domains
               CATH domains 1o5bB01     1o5bB02 B:28-120 Trypsin-like serine proteases                                                             1o5bB01 B:16-27,B:121-242 Trypsin-like serine proteases                                                                        CATH domains
               Pfam domains Trypsin-1o5bB01 B:16-238                                                                                                                                                                                                                         ---- Pfam domains
         Sec.struct. author ....ee.hhhhh..eeeeeee.....eeeeeeeeeee..eeeehhhhh....hhh.eeeee............eeeeeeeeee....ee....ee...eeeeee.............................eeeeee...............eeeeeeeehhhhhh....hhhhh...eeeee...............eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------M----------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-242 UniProt: 179-424                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) -----------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------ PROSITE (2)
           Transcript 1 (1) ------------------------------------------------Exon 1.10  PDB: B:60-104 UniProt: 227-277          ----------------------------------------------Exon 1.13  PDB: B:147-192 UniProt: 324-373        Exon 1.14d  PDB: B:193-242 (gaps) UniProt: 374-431 Transcript 1 (1)
           Transcript 1 (2) Exon 1.9b  PDB: B:16-60 UniProt: 154-227         -------------------------------------------------Exon 1.11  PDB: B:104-147 UniProt: 277-324      --------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1o5b B   16 IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLMSPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICLPSMYNDPQFGTSCEITGFGKEASTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDACQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHT  242
                                    25        35  ||||  41        51       60A||  |   67        77        87        97||     105     ||111       121       131       141       151       161      170A|      179      |187       197       207       217|    | 227       237     
                                                37A|||                     60A||  |                                 97A|          110A|||                                                         170A|            185A|                             217| 223A                   
                                                 37B||                      60B|  |                                  97B           110B||                                                          170B             185B                              219                        
                                                  37C|                       60C  |                                                 110C|                                                                                                                                        
                                                   37D                          62A                                                  110D

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Urokinase-type plasminogen activator (LMW U-PA), catalytic domain (66)

Human (Homo sapiens) [TaxId: 9606] (66)

d1o5b.1

A:,B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Human (Homo sapiens) (615)

1a	1o5bB02	B:28-120
1b	1o5bB01	B:16-27,B:121-242

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

Trypsin-1o5bB01

B:16-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (UROK_HUMAN | P00749)

molecular function
	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: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: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).
	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:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of 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).
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0071498	cellular response to fluid shear stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
	GO:0071333	cellular response to glucose stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
	GO:0035729	cellular response to hepatocyte growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus.
	GO:0071456	cellular response to hypoxia	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0071310	cellular response to organic substance	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0072734	cellular response to staurosporine	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a staurosporine stimulus.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0007566	embryo implantation	Attachment of the blastocyst to the uterine lining.
	GO:0042730	fibrinolysis	A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0070997	neuron death	The process of cell death in a neuron.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0060279	positive regulation of ovulation	Any process that activates or increases the frequency, rate or extent of ovulation, the release of a mature ovum/oocyte from an ovary.
	GO:2000379	positive regulation of reactive oxygen species metabolic process	Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
	GO:0014911	positive regulation of smooth muscle cell migration	Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0033628	regulation of cell adhesion mediated by integrin	Any process that modulates the frequency, rate, or extent of cell adhesion mediated by integrin.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:2000345	regulation of hepatocyte proliferation	Any process that modulates the frequency, rate or extent of hepatocyte proliferation.
	GO:0010469	regulation of receptor activity	Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0014910	regulation of smooth muscle cell migration	Any process that modulates the frequency, rate or extent of smooth muscle cell migration.
	GO:2000097	regulation of smooth muscle cell-matrix adhesion	Any process that modulates the frequency, rate or extent of smooth muscle cell-matrix adhesion.
	GO:0061041	regulation of wound healing	Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
	GO:0014823	response to activity	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 activity stimulus.
	GO:0035728	response to hepatocyte growth factor	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 hepatocyte growth factor stimulus.
	GO:0055093	response to hyperoxia	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 stimulus indicating increased oxygen tension.
	GO:0001666	response to hypoxia	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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0043403	skeletal muscle tissue regeneration	The regrowth of skeletal muscle tissue to repair injured or damaged muscle fibers in the postnatal stage.
	GO:0014909	smooth muscle cell migration	The orderly movement of a smooth muscle cell from one site to another, often during the development of a multicellular organism.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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: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:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	1o5b
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1gjc	1GJC IS THE WT ENZYME COMPLEXED WITH THE SAME INHIBITOR (CRA-8696)

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

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Exons (5, 6)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File