1YBW - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PROTEASE DOMAIN OF HGFA WITH NO INHIBITOR

Authors :   S. Shia, J. Stamos, D. Kirchhofer, B. Fan, J. Wu, R. T. Corpuz, L. Santell R. A. Lazarus, C. Eigenbrot

Date :   21 Dec 04 (Deposition) - 15 Feb 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Shia, J. Stamos, D. Kirchhofer, B. Fan, J. Wu, R. T. Corpuz, L. Santell, R. A. Lazarus, C. Eigenbrot
Conformational Lability In Serine Protease Active Sites: Structures Of Hepatocyte Growth Factor Activator (Hgfa) Alone And With The Inhibitory Domain From Hgfa Inhibitor-1B
J. Mol. Biol. V. 346 1335 2005
PubMed-ID: 15713485 | Reference-DOI: 10.1016/J.JMB.2004.12.048

Molecule 1 - HEPATOCYTE GROWTH FACTOR ACTIVATOR PRECURSOR
	Chains	:	A, B
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7108
	Expression System Vector Type	:	VIRUS
	Gene	:	HGFAC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HGF ACTIVATOR, HGFA

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:54 , PHE A:467 , ASN A:468	BINDING SITE FOR RESIDUE NAG A 741
2	AC2	SOFTWARE	HOH B:153 , PHE B:467 , ASN B:468	BINDING SITE FOR RESIDUE NAG B 742

Asymmetric Unit

No.	Residues
1	A:394	-	A:521
2	A:432	-	A:448
3	A:440	-	A:510
4	A:535	-	A:604
5	A:567	-	A:583
6	B:394	-	B:521
7	B:432	-	B:448
8	B:440	-	B:510
9	B:535	-	B:604
10	B:567	-	B:583

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

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024294	R	509	H	HGFA_HUMAN	Polymorphism	16844401	A/B	R	509	H
2	UniProt	VAR_024295	R	644	Q	HGFA_HUMAN	Polymorphism	2498323	A/B	R	644	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_024294	R	509	H	HGFA_HUMAN	Polymorphism	16844401	A	R	509	H
2	UniProt	VAR_024295	R	644	Q	HGFA_HUMAN	Polymorphism	2498323	A	R	644	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_024294	R	509	H	HGFA_HUMAN	Polymorphism	16844401	B	R	509	H
2	UniProt	VAR_024295	R	644	Q	HGFA_HUMAN	Polymorphism	2498323	B	R	644	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.	HGFA_HUMAN	408-646	2	A:408-645 B:408-645
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	HGFA_HUMAN	443-448	2	A:443-448 B:443-448
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	HGFA_HUMAN	592-603	2	A:592-603 B:592-603

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.	HGFA_HUMAN	408-646	1	A:408-645 -
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	HGFA_HUMAN	443-448	1	A:443-448 -
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	HGFA_HUMAN	592-603	1	A:592-603 -

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.	HGFA_HUMAN	408-646	1	- B:408-645
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	HGFA_HUMAN	443-448	1	- B:443-448
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	HGFA_HUMAN	592-603	1	- B:592-603

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000382774	1a	ENSE00001493344	chr4:3443614-3443845	232	HGFA_HUMAN	1-39	39	0	-	-
1.2	ENST00000382774	2	ENSE00000699356	chr4:3444459-3444639	181	HGFA_HUMAN	40-100	61	0	-	-
1.3	ENST00000382774	3	ENSE00000699357	chr4:3444777-3444873	97	HGFA_HUMAN	100-132	33	0	-	-
1.4	ENST00000382774	4	ENSE00000699358	chr4:3445068-3445147	80	HGFA_HUMAN	132-159	28	0	-	-
1.5	ENST00000382774	5	ENSE00000699359	chr4:3445766-3445888	123	HGFA_HUMAN	159-200	42	0	-	-
1.6a	ENST00000382774	6a	ENSE00000699360	chr4:3446038-3446169	132	HGFA_HUMAN	200-244	45	0	-	-
1.7	ENST00000382774	7	ENSE00001267259	chr4:3446350-3446460	111	HGFA_HUMAN	244-281	38	0	-	-
1.8	ENST00000382774	8	ENSE00001267254	chr4:3446546-3446720	175	HGFA_HUMAN	281-339	59	0	-	-
1.9a	ENST00000382774	9a	ENSE00000699364	chr4:3446992-3447077	86	HGFA_HUMAN	339-368	30	0	-	-
1.10b	ENST00000382774	10b	ENSE00000699365	chr4:3447769-3448021	253	HGFA_HUMAN	368-452	85	2	A:393-452 (gaps) B:393-452 (gaps)	60 60
1.11	ENST00000382774	11	ENSE00000699367	chr4:3449219-3449358	140	HGFA_HUMAN	452-499	48	2	A:452-499 B:452-499	48 48
1.12	ENST00000382774	12	ENSE00000699371	chr4:3449622-3449762	141	HGFA_HUMAN	499-546	48	2	A:499-546 B:499-546	48 48
1.13b	ENST00000382774	13b	ENSE00000699372	chr4:3449855-3450003	149	HGFA_HUMAN	546-595	50	2	A:546-595 B:546-595	50 50
1.14c	ENST00000382774	14c	ENSE00001493333	chr4:3450964-3451211	248	HGFA_HUMAN	596-655	60	2	A:596-645 B:596-645	50 50

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:246
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:253
                                   402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642   
           HGFA_HUMAN   393 ACGRRHKKRTFLRPRIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRI 645
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------1ybwA01     1ybwA02 A:420-519,A:634-645 Trypsin-like serine proteases                                           1ybwA01 A:408-419,A:520-633 Trypsin-like serine proteases                                                         1ybwA02      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........-------....ee........eeeeee..eeeeeeeee..eeeehhhhh....hhh.eeeee............eee.eeeeee..............eeeee..............................eeeeee...............eeeeee..hhhhhhh...........eeee................eeeeee..eeeeeeee............eeeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------------------------------------------Q- SAPs(SNPs)
                PROSITE (1) ---------------TRYPSIN_DOM  PDB: A:408-645 UniProt: 408-646                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) --------------------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.10b  PDB: A:393-452 (gaps) UniProt: 368-452          ----------------------------------------------Exon 1.12  PDB: A:499-546 UniProt: 499-546      -------------------------------------------------Exon 1.14c  PDB: A:596-645 UniProt: 596-655        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.11  PDB: A:452-499 UniProt: 452-499      ----------------------------------------------Exon 1.13b  PDB: A:546-595 UniProt: 546-595       -------------------------------------------------- Transcript 1 (2)
                 1ybw A 393 ACGRRHKK-------IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRI 645
                                   | -     | 412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642   
                                 400     408

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:253
                                   402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642   
           HGFA_HUMAN   393 ACGRRHKKRTFLRPRIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRI 645
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------1ybwB01     1ybwB02 B:420-519,B:634-645 Trypsin-like serine proteases                                           1ybwB01 B:408-419,B:520-633 Trypsin-like serine proteases                                                         1ybwB02      CATH domains
           Pfam domains (1) ---------------Trypsin-1ybwB01 B:408-641                                                                                                                                                                                                                 ---- Pfam domains (1)
           Pfam domains (2) ---------------Trypsin-1ybwB02 B:408-641                                                                                                                                                                                                                 ---- Pfam domains (2)
         Sec.struct. author ........-------....ee........eeeeee..eeeeeeeee..eeeehhhhh....hhh.eeeee............eee.eeeeee..............eeeee..............................eeeeee...............eeeeee..hhhhhhh...........eeee................eeeeee..eeeeeeee............eeeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------------------------------------------Q- SAPs(SNPs)
                PROSITE (1) ---------------TRYPSIN_DOM  PDB: B:408-645 UniProt: 408-646                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) --------------------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.10b  PDB: B:393-452 (gaps) UniProt: 368-452          ----------------------------------------------Exon 1.12  PDB: B:499-546 UniProt: 499-546      -------------------------------------------------Exon 1.14c  PDB: B:596-645 UniProt: 596-655        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.11  PDB: B:452-499 UniProt: 452-499      ----------------------------------------------Exon 1.13b  PDB: B:546-595 UniProt: 546-595       -------------------------------------------------- Transcript 1 (2)
                 1ybw B 393 ACGRRHKK-------IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRI 645
                                   | -     | 412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642   
                                 400     408

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 1YBW)

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	1ybwA01	A:408-419,A:520-633
1b	1ybwB01	B:408-419,B:520-633
1c	1ybwA02	A:420-519,A:634-645
1d	1ybwB02	B:420-519,B:634-645

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

1a	Trypsin-1ybwB01	B:408-641
1b	Trypsin-1ybwB02	B:408-641

Asymmetric Unit(hide GO term definitions)

Chain A,B (HGFA_HUMAN | Q04756)

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: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: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.
	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.

Asymmetric Unit
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	1ybw
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	HGFA_HUMAN \| Q04756	:	1yc0 2r0k 2r0l 2wub 2wuc 3k2u

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

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (10, 10)

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