3OND - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LUPINUS LUTEUS S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE IN COMPLEX WITH ADENOSINE

Authors :   K. Brzezinski, M. Jaskolski

Date :   28 Aug 10 (Deposition) - 31 Aug 11 (Release) - 19 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.17

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

Keywords :   Plant Protein, Enzyme-Substrate Complex, Nad Cofactor, Regulation Of Sam-Dependent Methylation Reactions (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Brzezinski, Z. Dauter, M. Jaskolski
High-Resolution Structures Of Complexes Of Plant S-Adenosyl-L-Homocysteine Hydrolase (Lupinus Luteus).
Acta Crystallogr. , Sect. D V. 68 218 2012
PubMed-ID: 22349223 | Reference-DOI: 10.1107/S0907444911055090
(for further references see the PDB file header)

Molecule 1 - ADENOSYLHOMOCYSTEINASE
	Chains	:	A, B
	EC Number	:	3.3.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIPL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	SAHH, SHH, SHH-1
	Organism Common	:	EUROPEAN YELLOW LUPIN
	Organism Scientific	:	LUPINUS LUTEUS
	Organism Taxid	:	3873
	Synonym	:	ADOHCYASE, SAHASE, S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	ADN	2	Ligand/Ion	ADENOSINE
2	NA	2	Ligand/Ion	SODIUM ION
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	ADN	4	Ligand/Ion	ADENOSINE
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	TRS	6	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	ADN	2	Ligand/Ion	ADENOSINE
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:206 , THR A:207 , THR A:208 , ASN A:240 , GLY A:269 , GLY A:271 , ASP A:272 , VAL A:273 , THR A:291 , GLU A:292 , ILE A:293 , ASP A:294 , CYS A:297 , THR A:324 , THR A:325 , GLY A:326 , ASN A:327 , ILE A:330 , ILE A:348 , GLY A:349 , HIS A:350 , ASN A:397 , HIS A:404 , ADN A:506 , HOH A:556 , HOH A:563 , HOH A:627 , HOH A:639 , HOH A:662 , HOH A:679 , HOH A:713 , GLN B:466 , LYS B:479 , TYR B:483	BINDING SITE FOR RESIDUE NAD A 501
2	AC2	SOFTWARE	THR A:460 , VAL A:474 , GLU A:475 , TYR A:478 , HOH A:540 , HOH A:588 , HOH A:1355 , HOH B:644	BINDING SITE FOR RESIDUE TRS A 505
3	AC3	SOFTWARE	HIS A:62 , THR A:64 , GLN A:66 , THR A:67 , ASP A:139 , GLU A:205 , THR A:206 , LYS A:235 , ASP A:239 , THR A:402 , HIS A:404 , MET A:409 , PHE A:413 , NAD A:501 , HOH A:859 , HOH A:963	BINDING SITE FOR RESIDUE ADN A 506
4	AC4	SOFTWARE	THR A:402 , GLY A:403 , HIS A:404 , HOH A:607 , HOH A:765	BINDING SITE FOR RESIDUE NA A 509
5	AC5	SOFTWARE	GLN A:466 , LYS A:479 , TYR A:483 , THR B:206 , THR B:207 , THR B:208 , ASN B:240 , GLY B:269 , GLY B:271 , ASP B:272 , VAL B:273 , THR B:291 , GLU B:292 , ILE B:293 , ASP B:294 , CYS B:297 , THR B:324 , THR B:325 , GLY B:326 , ASN B:327 , ILE B:330 , ILE B:348 , GLY B:349 , HIS B:350 , ASN B:397 , HIS B:404 , HOH B:498 , HOH B:499 , HOH B:501 , ADN B:507 , HOH B:525 , HOH B:587 , HOH B:761 , HOH B:785	BINDING SITE FOR RESIDUE NAD B 502
6	AC6	SOFTWARE	HOH A:595 , THR B:460 , VAL B:474 , GLU B:475 , TYR B:478 , HOH B:574 , HOH B:631 , HOH B:884 , HOH B:1262	BINDING SITE FOR RESIDUE TRS B 503
7	AC7	SOFTWARE	GLU B:361 , VAL B:366 , LYS B:367 , ARG B:368 , TRP B:378 , HOH B:751 , HOH B:1241 , HOH B:1242 , HOH B:1243 , HOH B:1254 , HOH B:1255	BINDING SITE FOR RESIDUE TRS B 504
8	AC8	SOFTWARE	HIS B:62 , THR B:64 , GLN B:66 , THR B:67 , ASP B:139 , GLU B:205 , THR B:206 , LYS B:235 , ASP B:239 , LEU B:395 , THR B:402 , HIS B:404 , MET B:409 , PHE B:413 , NAD B:502 , HOH B:592 , HOH B:694	BINDING SITE FOR RESIDUE ADN B 507
9	AC9	SOFTWARE	THR B:402 , GLY B:403 , HIS B:404 , HOH B:603 , HOH B:865	BINDING SITE FOR RESIDUE NA B 508

(no "SS Bond" information available for 3OND)

Asymmetric Unit

No.	Residues
1	Gly A:132	-	Pro A:133
2	Gly A:476	-	Pro A:477
3	Gly B:132	-	Pro B:133
4	Gly B:476	-	Pro B:477

(no "SAP(SNP)/Variant" information available for 3OND)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADOHCYASE_1	PS00738	S-adenosyl-L-homocysteine hydrolase signature 1.	SAHH_LUPLU	85-99	2	A:85-99 B:85-99
2	ADOHCYASE_2	PS00739	S-adenosyl-L-homocysteine hydrolase signature 2.	SAHH_LUPLU	262-279	2	A:262-279 B:262-279

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADOHCYASE_1	PS00738	S-adenosyl-L-homocysteine hydrolase signature 1.	SAHH_LUPLU	85-99	4	A:85-99 B:85-99
2	ADOHCYASE_2	PS00739	S-adenosyl-L-homocysteine hydrolase signature 2.	SAHH_LUPLU	262-279	4	A:262-279 B:262-279

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADOHCYASE_1	PS00738	S-adenosyl-L-homocysteine hydrolase signature 1.	SAHH_LUPLU	85-99	2	A:85-99 B:85-99
2	ADOHCYASE_2	PS00739	S-adenosyl-L-homocysteine hydrolase signature 2.	SAHH_LUPLU	262-279	2	A:262-279 B:262-279

(no "Exon" information available for 3OND)

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:487
 aligned with SAHH_LUPLU | Q9SP37 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:487
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       
           SAHH_LUPLU     - --MALLVEKTTSGREYKVKDMSQADFGRLEIELAEVEMPGLMASRSEFGPSQPFKGAKITGSLHMTIQTAVLIETLTALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDTTLLIHEGVKAEEIYEKSGQFPDPDSTDNAEFKIVLSIIKEGLKTDPKRYHKMKDRVVGVSEETTTGVKRLYQMQANGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVVAGYGDVGKGCAAALKQAGARVIVTEIDPICALQATMEGLQVLTLEDVVSEADIFVTTTGNKDIIMLDHMKKMKNNAIVCNIGHFDNEIDMLGLETHPGVKRITIKPQTDRWVFPETNTGIIILAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKSSGKYEKKVYVLPKHLDEKVAALHLEKLGAKLTKLSKDQADYISVPVEGPYKPFHYRY 485
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhh.eeee.hhhhhhhhhhhhhh......eee...hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhh.....eeee........hhhhhh.....eeeee........hhhhhhh....eeeeee..eeeee......eeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........ee..hhhhhhhhhhhhhhhhh......hhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------ADOHCYASE_1    ------------------------------------------------------------------------------------------------------------------------------------------------------------------ADOHCYASE_2       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ond A  -1 SHMALLVEKTTSGREYKVKDMSQADFGRLEIELAEVEMPGLMASRSEFGPSQPFKGAKITGSLHMTIQTAVLIETLTALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDTTLLIHEGVKAEEIYEKSGQFPDPDSTDNAEFKIVLSIIKEGLKTDPKRYHKMKDRVVGVSEETTTGVKRLYQMQANGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVVAGYGDVGKGCAAALKQAGARVIVTEIDPICALQATMEGLQVLTLEDVVSEADIFVTTTGNKDIIMLDHMKKMKNNAIVCNIGHFDNEIDMLGLETHPGVKRITIKPQTDRWVFPETNTGIIILAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKSSGKYEKKVYVLPKHLDEKVAALHLEKLGAKLTKLSKDQADYISVPVEGPYKPFHYRY 485
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478

Chain B from PDB  Type:PROTEIN  Length:488
 aligned with SAHH_LUPLU | Q9SP37 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:488
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477        
           SAHH_LUPLU     - ---MALLVEKTTSGREYKVKDMSQADFGRLEIELAEVEMPGLMASRSEFGPSQPFKGAKITGSLHMTIQTAVLIETLTALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDTTLLIHEGVKAEEIYEKSGQFPDPDSTDNAEFKIVLSIIKEGLKTDPKRYHKMKDRVVGVSEETTTGVKRLYQMQANGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVVAGYGDVGKGCAAALKQAGARVIVTEIDPICALQATMEGLQVLTLEDVVSEADIFVTTTGNKDIIMLDHMKKMKNNAIVCNIGHFDNEIDMLGLETHPGVKRITIKPQTDRWVFPETNTGIIILAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKSSGKYEKKVYVLPKHLDEKVAALHLEKLGAKLTKLSKDQADYISVPVEGPYKPFHYRY 485
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhh.eeee.hhhhhhhhhhhhhh......eee...hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhh.....eeee........hhhhhh.....eeeee........hhhhhhh....eeeeee..eeeeee....eeeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........ee..hhhhhhhhhhhhhhhhh......hhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------ADOHCYASE_1    ------------------------------------------------------------------------------------------------------------------------------------------------------------------ADOHCYASE_2       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ond B  -2 GSHMALLVEKTTSGREYKVKDMSQADFGRLEIELAEVEMPGLMASRSEFGPSQPFKGAKITGSLHMTIQTAVLIETLTALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDTTLLIHEGVKAEEIYEKSGQFPDPDSTDNAEFKIVLSIIKEGLKTDPKRYHKMKDRVVGVSEETTTGVKRLYQMQANGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVVAGYGDVGKGCAAALKQAGARVIVTEIDPICALQATMEGLQVLTLEDVVSEADIFVTTTGNKDIIMLDHMKKMKNNAIVCNIGHFDNEIDMLGLETHPGVKRITIKPQTDRWVFPETNTGIIILAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKSSGKYEKKVYVLPKHLDEKVAALHLEKLGAKLTKLSKDQADYISVPVEGPYKPFHYRY 485
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477

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 "SCOP Domain" information available for 3OND)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (SAHH_LUPLU | Q9SP37)

molecular function
	GO:0004013	adenosylhomocysteinase activity	Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenosine + L-homocysteine.
	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.
biological process
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:132 - Pro A:133	[ RasMol ]
		Gly A:476 - Pro A:477	[ RasMol ]
		Gly B:132 - Pro B:133	[ RasMol ]
		Gly B:476 - Pro B:477	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3ond
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	SAHH_LUPLU \| Q9SP37
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	3.3.1.1
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	SAHH_LUPLU \| Q9SP37
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UniProtKB/Swiss-Prot
	SAHH_LUPLU \| Q9SP37	:	3one 3onf

1a7a	STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DETERMINATION OF A 30 SELENIUM ATOM SUBSTRUCTURE FROM DATA AT A SINGLE WAVELENGTH
1b3r	RAT LIVER S-ADENOSYLHOMOCYSTEINE HYDROLASE
1v8b	CRYSTAL STRUCTURE OF S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE FROM THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM
3ce6	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS S-ADENOSYL- L-HOMOCYSTEINE HYDROLASE IN TERNARY COMPLEX WITH NAD AND ADENOSINE
3one	CRYSTAL STRUCTURE OF LUPINUS LUTEUS S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE IN COMPLEX WITH ADENINE
3onf	CRYSTAL STRUCTURE OF LUPINUS LUTEUS S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE IN COMPLEX WITH CORDYCEPIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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Related Entries Specified in the PDB File