1CQD - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, ZINGIBER OFFICINALE

Authors :   K. H. Choi, R. A. Laursen, K. N. Allen

Date :   15 Jun 99 (Deposition) - 28 Sep 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Cysteine Protease, Glycoprotein, Proline Specificity, Carbohydrate, Papain Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Choi, R. A. Laursen, K. N. Allen
The 2. 1 A Structure Of A Cysteine Protease With Proline Specificity From Ginger Rhizome, Zingiber Officinale.
Biochemistry V. 38 11624 1999
PubMed-ID: 10512617 | Reference-DOI: 10.1021/BI990651B

Molecule 1 - PROTEIN (PROTEASE II)
	Chains	:	A, B, C, D
	Organism Scientific	:	ZINGIBER OFFICINALE
	Organism Taxid	:	94328
	Other Details	:	TETRATHIONATE ATTACHED TO CYS-27
	Other Details - Source	:	PURIFIED FROM GROUND GINGER ROOT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 19)

No.	Name	Count	Type	Full Name
1	FUC	3	Ligand/Ion	ALPHA-L-FUCOSE
2	FUL	1	Ligand/Ion	BETA-L-FUCOSE
3	NAG	11	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	THJ	4	Ligand/Ion	THIOSULFATE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	FUC	-1	Ligand/Ion	ALPHA-L-FUCOSE
2	FUL	1	Ligand/Ion	BETA-L-FUCOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	THJ	1	Ligand/Ion	THIOSULFATE

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
2	FUL	-1	Ligand/Ion	BETA-L-FUCOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	THJ	1	Ligand/Ion	THIOSULFATE

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
2	FUL	-1	Ligand/Ion	BETA-L-FUCOSE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	THJ	1	Ligand/Ion	THIOSULFATE

Biological Unit 4 (3, 4)

No.	Name	Count	Type	Full Name
1	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
2	FUL	-1	Ligand/Ion	BETA-L-FUCOSE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	THJ	1	Ligand/Ion	THIOSULFATE

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:156 , ILE A:157 , ASN A:201 , FUL A:501 , NAG A:503 , VAL D:43 , THR D:44	BINDING SITE FOR RESIDUE NAG A 500
02	AC2	SOFTWARE	NAG A:500 , NAG A:503	BINDING SITE FOR RESIDUE FUL A 501
03	AC3	SOFTWARE	NAG A:500 , FUL A:501	BINDING SITE FOR RESIDUE NAG A 503
04	AC4	SOFTWARE	ASN A:99 , NAG A:901	BINDING SITE FOR RESIDUE NAG A 900
05	AC5	SOFTWARE	NAG A:900	BINDING SITE FOR RESIDUE NAG A 901
06	AC6	SOFTWARE	CYS B:155 , ASN B:156 , FUC B:501 , NAG B:503 , VAL C:43 , THR C:44	BINDING SITE FOR RESIDUE NAG B 500
07	AC7	SOFTWARE	NAG B:500 , NAG B:503	BINDING SITE FOR RESIDUE FUC B 501
08	AC8	SOFTWARE	NAG B:500 , FUC B:501	BINDING SITE FOR RESIDUE NAG B 503
09	AC9	SOFTWARE	ILE B:97 , ASN B:99	BINDING SITE FOR RESIDUE NAG B 900
10	BC1	SOFTWARE	ASN C:99 , THR C:101 , NAG C:901 , FUC C:902	BINDING SITE FOR RESIDUE NAG C 900
11	BC2	SOFTWARE	NAG C:900	BINDING SITE FOR RESIDUE NAG C 901
12	BC3	SOFTWARE	NAG C:900	BINDING SITE FOR RESIDUE FUC C 902
13	BC4	SOFTWARE	ILE D:97 , ASN D:99 , THR D:101 , NAG D:901 , FUC D:902	BINDING SITE FOR RESIDUE NAG D 900
14	BC5	SOFTWARE	NAG D:900	BINDING SITE FOR RESIDUE FUC D 902
15	BC6	SOFTWARE	NAG D:900	BINDING SITE FOR RESIDUE NAG D 901
16	BC7	SOFTWARE	GLN A:21 , GLY A:25 , SER A:26 , CYS A:27 , ASN A:160 , HIS A:161 , HOH A:904	BINDING SITE FOR RESIDUE THJ A 800
17	BC8	SOFTWARE	GLN B:21 , GLY B:25 , SER B:26 , CYS B:27 , ASN B:160 , HIS B:161	BINDING SITE FOR RESIDUE THJ B 800
18	BC9	SOFTWARE	GLN C:21 , GLY C:25 , SER C:26 , CYS C:27 , ASN C:160 , HIS C:161 , HOH C:973	BINDING SITE FOR RESIDUE THJ C 800
19	CAA	AUTHOR	CYS A:27 , HIS A:161	CYS 27 AND HIS 161 ARE THE CATALYTIC DIAD.
20	CAB	AUTHOR	CYS B:27 , HIS B:161	CYS 27 AND HIS 161 ARE THE CATALYTIC DIAD.
21	CAC	AUTHOR	CYS C:27 , HIS C:161	CYS 27 AND HIS 161 ARE THE CATALYTIC DIAD.
22	CAD	AUTHOR	CYS D:27 , HIS D:161	CYS 27 AND HIS 161 ARE THE CATALYTIC DIAD.
23	CC1	SOFTWARE	GLN D:21 , GLY D:25 , SER D:26 , CYS D:27 , ASN D:160 , HIS D:161	BINDING SITE FOR RESIDUE THJ D 800

Asymmetric Unit

No.	Residues
1	A:24	-	A:65
2	A:58	-	A:98
3	A:155	-	A:206
4	B:24	-	B:65
5	B:58	-	B:98
6	B:155	-	B:206
7	C:24	-	C:65
8	C:58	-	C:98
9	C:155	-	C:206
10	D:24	-	D:65
11	D:58	-	D:98
12	D:155	-	D:206

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

(no "SAP(SNP)/Variant" information available for 1CQD)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CPGP2_ZINOF	21-32	4	A:21-32 B:21-32 C:21-32 D:21-32
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CPGP2_ZINOF	159-169	4	A:159-169 B:159-169 C:159-169 D:159-169

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CPGP2_ZINOF	21-32	1	A:21-32 - - -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CPGP2_ZINOF	159-169	1	A:159-169 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CPGP2_ZINOF	21-32	1	- B:21-32 - -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CPGP2_ZINOF	159-169	1	- B:159-169 - -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CPGP2_ZINOF	21-32	1	- - C:21-32 -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CPGP2_ZINOF	159-169	1	- - C:159-169 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CPGP2_ZINOF	21-32	1	- - - D:21-32
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CPGP2_ZINOF	159-169	1	- - - D:159-169

(no "Exon" information available for 1CQD)

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:216
 aligned with CPGP2_ZINOF | P82474 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
          CPGP2_ZINOF     3 LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKK 218
               SCOP domains d1cqda_ A: Proline-specific cysteine protease                                                                                                                                                                            SCOP domains
               CATH domains 1cqdA00 A:3-218 Cysteine proteinases                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh..............................eeee.....hhhhhhhh....eeeee....hhhh................eeeeeeeeeee..eeeeeee...........eeeee........hhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cqd A   3 LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKK 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with CPGP2_ZINOF | P82474 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
          CPGP2_ZINOF     3 LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKK 218
               SCOP domains d1cqdb_ B: Proline-specific cysteine protease                                                                                                                                                                            SCOP domains
               CATH domains 1cqdB00 B:3-218 Cysteine proteinases                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh..............................eeee.....hhhhhhhh....eeeee....hhhh................eeeeeeeeeee..eeeeeee...........eeeee........hhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cqd B   3 LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKK 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain C from PDB  Type:PROTEIN  Length:216
 aligned with CPGP2_ZINOF | P82474 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
          CPGP2_ZINOF     3 LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKK 218
               SCOP domains d1cqdc_ C: Proline-specific cysteine protease                                                                                                                                                                            SCOP domains
               CATH domains 1cqdC00 C:3-218 Cysteine proteinases                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh..............................eeee.....hhhhhhhh....eeeee....hhhh................eeeeeeeeeee..eeeeeee...........eeeee........hhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cqd C   3 LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKK 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain D from PDB  Type:PROTEIN  Length:216
 aligned with CPGP2_ZINOF | P82474 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
          CPGP2_ZINOF     3 LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKK 218
               SCOP domains d1cqdd_ D: Proline-specific cysteine protease                                                                                                                                                                            SCOP domains
               CATH domains 1cqdD00 D:3-218 Cysteine proteinases                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh..............................eeee.....hhhhhhhh....eeeee....hhhh................eeeeeeeeeee..eeeeeee...........eeeee........hhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cqd D   3 LPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKK 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Legend:		→ Mismatch	(orange background)
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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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Papain-like (200)

Protein domain: Proline-specific cysteine protease (1)

Ginger rhizome (Zingiber officinale) [TaxId: 94328] (1)

1a	d1cqda_	A:
1b	d1cqdb_	B:
1c	d1cqdc_	C:
1d	d1cqdd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Cathepsin B; Chain A (207)

Homologous Superfamily: Cysteine proteinases (207)

Zingiber officinale. Organism_taxid: 94328. (1)

1a	1cqdA00	A:3-218
1b	1cqdB00	B:3-218
1c	1cqdC00	C:3-218
1d	1cqdD00	D:3-218

(no "Pfam Domain" information available for 1CQD)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CPGP2_ZINOF | P82474)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	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.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric Unit
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	Cis Peptide Bonds
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	1cqd
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	CPGP2_ZINOF \| P82474
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(no "Entries Sharing at Least One Protein Chain" available for 1CQD)

(no "Related Entries Specified in the PDB File" available for 1CQD)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (23, 23)

SS Bonds (12, 12)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File