3AH3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LR5-1, 3-ISOPROPYLMALATE DEHYDROGENASE CREATED BY DIRECTED EVOLUTION

Authors :   T. Tomita, Y. Suzuki, T. Kuzuyama, M. Nishiyama

Date :   13 Apr 10 (Deposition) - 02 Feb 11 (Release) - 02 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   3-Isopropylmalate Dehydrogenase, Homoisocitrate Dehydrogenase, Directed Evolution, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Suzuki, K. Asada, J. Miyazaki, T. Tomita, T. Kuzuyama, M. Nishiyama
Enhancement Of The Latent 3-Isopropylmalate Dehydrogenase Activity Of Promiscuous Homoisocitrate Dehydrogenase By Directed Evolution
Biochem. J. V. 431 401 2010
PubMed-ID: 20735360 | Reference-DOI: 10.1042/BJ20101246

Molecule 1 - HOMOISOCITRATE DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.87
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-LR5-1, PET 26B(+)
	Expression System Strain	:	BL21(DE3)RILCODONPLUS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LR5-1
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	262724
	Strain	:	HB27
	Synonym	:	LR5-1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A		C
Biological Unit 2 (2x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 15)

No.	Name	Count	Type	Full Name
1	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 14)

No.	Name	Count	Type	Full Name
1	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:131 , LYS C:144 , LEU C:181	BINDING SITE FOR RESIDUE SO4 A 335
02	AC2	SOFTWARE	GLU A:298	BINDING SITE FOR RESIDUE EDO A 336
03	AC3	SOFTWARE	ILE A:157	BINDING SITE FOR RESIDUE EDO A 337
04	AC4	SOFTWARE	ILE A:157	BINDING SITE FOR RESIDUE EDO A 338
05	AC5	SOFTWARE	ASN A:273	BINDING SITE FOR RESIDUE EDO A 339
06	AC6	SOFTWARE	ARG B:131 , HOH B:413 , LYS D:144 , LEU D:181	BINDING SITE FOR RESIDUE SO4 B 335
07	AC7	SOFTWARE	GLU B:298	BINDING SITE FOR RESIDUE EDO B 336
08	AC8	SOFTWARE	ILE B:157	BINDING SITE FOR RESIDUE EDO B 337
09	AC9	SOFTWARE	ALA B:272 , ASN B:273	BINDING SITE FOR RESIDUE EDO B 339
10	BC1	SOFTWARE	LYS A:144 , LEU A:181 , ARG C:131 , HOH C:351	BINDING SITE FOR RESIDUE SO4 C 335
11	BC2	SOFTWARE	ASP C:286 , GLU C:298	BINDING SITE FOR RESIDUE EDO C 336
12	BC3	SOFTWARE	LYS B:144 , ARG D:131 , HOH D:365	BINDING SITE FOR RESIDUE SO4 D 335
13	BC4	SOFTWARE	ASP D:286	BINDING SITE FOR RESIDUE EDO D 336

(no "SS Bond" information available for 3AH3)

Asymmetric Unit

No.	Residues
1	Pro A:78	-	Gly A:79
2	Gly A:79	-	Phe A:80
3	Gly A:308	-	Pro A:309
4	Gly B:308	-	Pro B:309
5	Gly C:308	-	Pro C:309
6	Phe D:81	-	Gly D:82
7	Gly D:308	-	Pro D:309

(no "SAP(SNP)/Variant" information available for 3AH3)

(no "PROSITE Motif" information available for 3AH3)

(no "Exon" information available for 3AH3)

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:333
 aligned with HICDH_THET2 | Q72IW9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:333
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
          HICDH_THET2     2 AYRICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSCHATLFGAATSPTRKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEALKSL 334
               SCOP domains d3ah3a_ A: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh...hhhhhhhhhh..eeeeee............hhhhhhhhhhh..eeeeeee...........eeeeeee.........eeee..eeeeeeeeehhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh......eeeee....eeeee....hhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ah3 A   2 AYRICLIEGDGIGYEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVVKILSCHATLFGAATIPTRKVPGFFGAIMALRRRLDLYANVRPAKSRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCATQLVMRPERYDVIVTTNLLGDILSDLAAGLMGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPMTPDLGGDATTEAFTEAVVEALKSL 334
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain B from PDB  Type:PROTEIN  Length:333
 aligned with HICDH_THET2 | Q72IW9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:333
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
          HICDH_THET2     2 AYRICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSCHATLFGAATSPTRKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEALKSL 334
               SCOP domains d3ah3b_ B: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh...hhhhhhhhhhh.eeeeee............hhhhhhhhhhh..eeeeeee...........eeeeeee.........eeee..eeeeeeeeehhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh......eeeee....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ah3 B   2 AYRICLIEGDGIGYEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVVKILSCHATLFGAATIPTRKVPGFFGAIMALRRRLDLYANVRPAKSRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCATQLVMRPERYDVIVTTNLLGDILSDLAAGLMGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPMTPDLGGDATTEAFTEAVVEALKSL 334
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain C from PDB  Type:PROTEIN  Length:333
 aligned with HICDH_THET2 | Q72IW9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:333
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
          HICDH_THET2     2 AYRICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSCHATLFGAATSPTRKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEALKSL 334
               SCOP domains d3ah3c_ C: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhh....eeeee...hhhhhhhhh...hhhhhhhhhh..eeeeee.............hhhhhhhhhh..eeeeeee...........eeeeeee.........eeee..eeeeeeeeehhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ah3 C   2 AYRICLIEGDGIGYEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVVKILSCHATLFGAATIPTRKVPGFFGAIMALRRRLDLYANVRPAKSRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCATQLVMRPERYDVIVTTNLLGDILSDLAAGLMGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPMTPDLGGDATTEAFTEAVVEALKSL 334
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain D from PDB  Type:PROTEIN  Length:333
 aligned with HICDH_THET2 | Q72IW9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:333
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
          HICDH_THET2     2 AYRICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSCHATLFGAATSPTRKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEALKSL 334
               SCOP domains d3ah3d_ D: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhh...hhhhhhhhhhh.eeeeee............hhhhhhhhhhh..eeeeeee...........eeeeeee.hhhh....eeee..eeeeeeeeehhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh.....eeeee....eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ah3 D   2 AYRICLIEGDGIGYEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVVKILSCHATLFGAATIPTRKVPGFFGAIMALRRRLDLYANVRPAKSRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCATQLVMRPERYDVIVTTNLLGDILSDLAAGLMGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPMTPDLGGDATTEAFTEAVVEALKSL 334
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Family: automated matches (22)

Protein domain: automated matches (22)

Thermus thermophilus [TaxId: 262724] (1)

1a	d3ah3a_	A:
1b	d3ah3b_	B:
1c	d3ah3c_	C:
1d	d3ah3d_	D:

(no "CATH Domain" information available for 3AH3)

(no "Pfam Domain" information available for 3AH3)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (HICDH_THET2 | Q72IW9)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0047046	homoisocitrate dehydrogenase activity	Catalysis of the reaction: NAD+ + 3-carboxy-2-hydroxyadipate = NADH + H+ + CO2 + 2-keto-adipate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0019878	lysine biosynthetic process via aminoadipic acid	The chemical reactions and pathways resulting in the formation of lysine by the aminoadipic pathway.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:308 - Pro A:309	[ RasMol ]
		Gly A:79 - Phe A:80	[ RasMol ]
		Gly B:308 - Pro B:309	[ RasMol ]
		Gly C:308 - Pro C:309	[ RasMol ]
		Gly D:308 - Pro D:309	[ RasMol ]
		Phe D:81 - Gly D:82	[ RasMol ]
		Pro A:78 - Gly A:79	[ RasMol ]

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	3ah3
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	HICDH_THET2 \| Q72IW9	:	1x0l 3asj 4yb4

1x0l	CRYSTAL STRUCTURE OF TETRAMERIC HOMOISOCITRATE DEHYDROGENASE FROM AN EXTREME THERMOPHILE, THERMUS THERMOPHILUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 15)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File