2BDG - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN KALLIKREIN 4 COMPLEX WITH NICKEL AND P-AMINOBENZAMIDINE

Authors :   M. Debela, W. Bode, P. Goettig, Structural Proteomics In Europe (S

Date :   20 Oct 05 (Deposition) - 03 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Serine Proteinase, S1 Subsite, 70-80 Loop, Structural Proteomics In Europe, Spine, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Debela, V. Magdolen, V. Grimminger, C. Sommerhoff, A. Messerschmidt, R. Huber, R. Friedrich, W. Bode, P. Goettig
Crystal Structures Of Human Tissue Kallikrein 4: Activity Modulation By A Specific Zinc Binding Site.
J. Mol. Biol. V. 362 1094 2006
PubMed-ID: 16950394 | Reference-DOI: 10.1016/J.JMB.2006.08.003

Molecule 1 - KALLIKREIN-4
	Chains	:	A, B
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	HUMAN KALLIKREIN 4
	Gene	:	KLK4, EMSP1, PRSS17, PSTS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROSTASE, KALLIKREIN-LIKE PROTEIN 1, KLK-L1, ENAMEL MATRIX SERINE PROTEINASE 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	NA	2	Ligand/Ion	SODIUM ION
3	NI	4	Ligand/Ion	NICKEL (II) ION
4	PBZ	2	Ligand/Ion	P-AMINO BENZAMIDINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	NI	-1	Ligand/Ion	NICKEL (II) ION
4	PBZ	1	Ligand/Ion	P-AMINO BENZAMIDINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	NI	-1	Ligand/Ion	NICKEL (II) ION
4	PBZ	1	Ligand/Ion	P-AMINO BENZAMIDINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:99 , ASP A:102 , MET A:180 , SER A:214 , HOH A:412	BINDING SITE FOR RESIDUE NA A 401
02	AC2	SOFTWARE	PRO A:129 , GLN A:210 , ASN A:230 , LEU A:231 , CYS A:232	BINDING SITE FOR RESIDUE NA A 402
03	AC3	SOFTWARE	LEU B:98 , SER B:164	BINDING SITE FOR RESIDUE CL B 403
04	AC4	SOFTWARE	LEU A:98 , VAL A:163 , SER A:164 , VAL A:167 , HOH A:498 , HOH A:529	BINDING SITE FOR RESIDUE CL A 404
05	AC5	SOFTWARE	HIS A:25 , GLU A:77 , HOH A:480 , HOH A:483 , HOH A:486 , HOH A:557 , HOH A:563	BINDING SITE FOR RESIDUE NI A 405
06	AC6	SOFTWARE	HIS B:25 , GLU B:77 , HOH B:534 , HOH B:535 , HOH B:536 , HOH B:537	BINDING SITE FOR RESIDUE NI B 406
07	AC7	SOFTWARE	THR B:64 , HOH B:538 , HOH B:539 , HOH B:540	BINDING SITE FOR RESIDUE NI B 407
08	AC8	SOFTWARE	ASN A:37 , HOH A:531 , HOH A:550 , HOH A:556 , HOH A:558 , HOH A:560	BINDING SITE FOR RESIDUE NI A 408
09	AC9	SOFTWARE	ASP A:189 , SER A:190 , ASN A:192 , SER A:195 , VAL A:213 , PHE A:215 , CYS A:220 , GLY A:226 , HOH A:424	BINDING SITE FOR RESIDUE PBZ A 301
10	BC1	SOFTWARE	ASP B:189 , SER B:190 , SER B:195 , VAL B:213 , PHE B:215 , GLY B:216 , LYS B:217 , CYS B:220 , GLY B:226 , HOH B:415	BINDING SITE FOR RESIDUE PBZ B 302

Asymmetric Unit

No.	Residues
1	A:22	-	A:157
2	A:42	-	A:58
3	A:128	-	A:232
4	A:136	-	A:201
5	A:168	-	A:182
6	A:191	-	A:220
7	B:22	-	B:157
8	B:42	-	B:58
9	B:128	-	B:232
10	B:136	-	B:201
11	B:168	-	B:182
12	B:191	-	B:220

Asymmetric Unit

No.	Residues
1	Arg A:96	-	Pro A:97
2	Asp A:173	-	Pro A:174
3	Ala A:218	-	Pro A:219
4	Arg B:96	-	Pro B:97
5	Asp B:173	-	Pro B:174
6	Ala B:218	-	Pro B:219

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033009	G	159	D	KLK4_HUMAN	Polymorphism	34626614	A/B	G	147	D
2	UniProt	VAR_028365	H	197	Q	KLK4_HUMAN	Polymorphism	2569527	A/B	Q	186A	Q

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033009	G	159	D	KLK4_HUMAN	Polymorphism	34626614	A	G	147	D
2	UniProt	VAR_028365	H	197	Q	KLK4_HUMAN	Polymorphism	2569527	A	Q	186A	Q

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_033009	G	159	D	KLK4_HUMAN	Polymorphism	34626614	B	G	147	D
2	UniProt	VAR_028365	H	197	Q	KLK4_HUMAN	Polymorphism	2569527	B	Q	186A	Q

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	KLK4_HUMAN	31-252	2	A:16-243 B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	KLK4_HUMAN	67-72	2	A:53-58 B:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	KLK4_HUMAN	201-212	2	A:189-200 B:189-200

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	KLK4_HUMAN	31-252	1	A:16-243 -
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	KLK4_HUMAN	67-72	1	A:53-58 -
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	KLK4_HUMAN	201-212	1	A:189-200 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	KLK4_HUMAN	31-252	1	- B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	KLK4_HUMAN	67-72	1	- B:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	KLK4_HUMAN	201-212	1	- B:189-200

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000324041	1	ENSE00001805755	chr19:51413994-51413934	61	KLK4_HUMAN	1-21	21	0	-	-
1.2	ENST00000324041	2	ENSE00001664323	chr19:51412670-51412508	163	KLK4_HUMAN	21-75	55	2	A:16-61 (gaps) B:16-61 (gaps)	46 46
1.3a	ENST00000324041	3a	ENSE00001265762	chr19:51412085-51411835	251	KLK4_HUMAN	75-159	85	2	A:61-147 (gaps) B:61-147 (gaps)	88 88
1.3c	ENST00000324041	3c	ENSE00001265832	chr19:51411751-51411615	137	KLK4_HUMAN	159-204	46	2	A:147-192 (gaps) B:147-192 (gaps)	48 48
1.4	ENST00000324041	4	ENSE00001265771	chr19:51410342-51409608	735	KLK4_HUMAN	205-254	50	2	A:193-244 (gaps) B:193-244 (gaps)	53 53

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:223
 aligned with KLK4_HUMAN | Q9Y5K2 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:223
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          KLK4_HUMAN     31 IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGHDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA  253
               SCOP domains d2bdga_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains 2bdgA01     2bdgA02 A:28-120,A:235-244 Trypsin-like serine proteases                                    2bdgA01 A:16-27,A:121-234 Trypsin-like serine proteases                                                      2bdgA02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee....eeeeeeeee..eeeehhhhh...eeeee.....hhhhh...eeeeeeeeee.............eeeee........................eeeeee.............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee...........eeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------D-------------------------------------Q-------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 31-252                                                                                                                                                                                    - PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-61 (gaps) UniProt: 21-75 -----------------------------------------------------------------------------------Exon 1.3c  PDB: A:147-192 (gaps)              Exon 1.4  PDB: A:193-244 (gaps) UniProt: 205-254  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3a  PDB: A:61-147 (gaps) UniProt: 75-159                                      ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                2bdg A   16 IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA  244
                                    25        35  ||    46        56        66||     |76        86        96       106       116       127  ||   138       150       160       170       180      |188       198    || 212       221       231       241   
                                                 38|                         67|   74A                                                125|  ||            147|                                 186A|              203|         220A                        
                                                  40                          69                                                       127  ||             150                                  186B               208                                     
                                                                                                                                          130|                                                                                                             
                                                                                                                                           132

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with KLK4_HUMAN | Q9Y5K2 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:223
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          KLK4_HUMAN     31 IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGHDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA  253
               SCOP domains d2bdgb_ B: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains 2bdgB01     2bdgB02 B:28-120,B:235-244 Trypsin-like serine proteases                                    2bdgB01 B:16-27,B:121-234 Trypsin-like serine proteases                                                      2bdgB02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee....eeeeeeeee..eeeehhhhh...eeeee.....hhhhh...eeeee.eeee.............eeee.........................eeeeee.............eeeeeeeehhhhhhhhhh......eeee................eeee..eeeeeeee...........eeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------D-------------------------------------Q-------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 31-252                                                                                                                                                                                    - PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:16-61 (gaps) UniProt: 21-75 -----------------------------------------------------------------------------------Exon 1.3c  PDB: B:147-192 (gaps)              Exon 1.4  PDB: B:193-244 (gaps) UniProt: 205-254  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3a  PDB: B:61-147 (gaps) UniProt: 75-159                                      ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                2bdg B   16 IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA  244
                                    25        35  ||    46        56        66||     |76        86        96       106       116       127  ||   138       150       160       170       180      |188       198    || 212       221       231       241   
                                                 38|                         67|   74A                                                125|  ||            147|                                 186A|              203|         220A                        
                                                  40                          69                                                       127  ||             150                                  186B               208                                     
                                                                                                                                          130|                                                                                                             
                                                                                                                                           132

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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: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: automated matches (71)

Protein domain: automated matches (71)

Human (Homo sapiens) [TaxId: 9606] (37)

1a	d2bdga_	A:
1b	d2bdgb_	B:

Asymmetric 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	2bdgA01	A:16-27,A:121-234
1b	2bdgB01	B:16-27,B:121-234
1c	2bdgA02	A:28-120,A:235-244
1d	2bdgB02	B:28-120,B:235-244

(no "Pfam Domain" information available for 2BDG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KLK4_HUMAN | Q9Y5K2)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0097186	amelogenesis	The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage.
	GO:0031214	biomineral tissue development	Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:218 - Pro A:219	[ RasMol ]
		Ala B:218 - Pro B:219	[ RasMol ]
		Arg A:96 - Pro A:97	[ RasMol ]
		Arg B:96 - Pro B:97	[ RasMol ]
		Asp A:173 - Pro A:174	[ RasMol ]
		Asp B:173 - Pro B:174	[ RasMol ]

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	2bdg
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	3.4.21.-
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	KLK4_HUMAN \| Q9Y5K2	:	2bdh 2bdi 4k1e 4k8y 4kel 4kga

(no "Related Entries Specified in the PDB File" available for 2BDG)

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (12, 12)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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