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Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF FACTOR XI IN COMPLEX WITH (R)-1-(4-(4-(HYDROXYMETHYL)-1,3,2-DIOXABOROLAN-2-YL)PHENETHYL)GUANIDINE

Authors :   T. I. Lazarova, L. Jin, M. J. Rynkiewicz, J. C. Gorga, F. Bibbins, H. V. Meyers, R. E. Babine, J. E. Strickler

Date :   10 May 05 (Deposition) - 09 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym./Biol. Unit : A

Keywords :   Fxi, Inhibitor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. I. Lazarova, L. Jin, M. Rynkiewicz, J. C. Gorga, F. Bibbins, H. V. Meyers, R. Babine, J. Strickler
Synthesis And In Vitro Biological Evaluation Of Aryl Boronic Acids As Potential Inhibitors Of Factor Xia.
Bioorg. Med. Chem. Lett. V. 16 5022 2006
PubMed-ID: 16876411 | Reference-DOI: 10.1016/J.BMCL.2006.07.043
(for further references see the PDB file header)

Molecule 1 - COAGULATION FACTOR XI
	Chains	:	A
	EC Number	:	3.4.21.27
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Strain	:	X-33
	Expression System Taxid	:	4922
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	F11
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PLASMA THROMBOPLASTIN ANTECEDENT, PTA, FXI

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	412	1	Ligand/Ion	(R)-1-(4-(4-(HYDROXYMETHYL)-1,3,2-DIOXABOROLAN-2-YL)PHENETHYL)GUANIDINE
2	BCT	1	Ligand/Ion	BICARBONATE ION
3	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:113 , TYR A:143 , ARG A:147 , LYS A:149 , LYS A:192	BINDING SITE FOR RESIDUE SO4 A 1002
2	AC2	SOFTWARE	VAL A:163 , GLU A:167 , ARG A:171 , GLY A:184 , TYR A:184A , ARG A:185 , GLU A:223 , PRO A:225 , HOH A:1137	BINDING SITE FOR RESIDUE SO4 A 1003
3	AC3	SOFTWARE	THR A:20 , ALA A:21 , GLN A:86 , LYS A:107 , HOH A:1164 , HOH A:1184	BINDING SITE FOR RESIDUE SO4 A 1004
4	AC4	SOFTWARE	PHE A:83 , ASN A:113 , GLN A:118 , HOH A:1166	BINDING SITE FOR RESIDUE BCT A 1005
5	AC5	SOFTWARE	GLU A:26 , TRP A:27 , TRP A:137 , TRP A:203 , HOH A:1154	BINDING SITE FOR RESIDUE SO4 A 1006
6	AC6	SOFTWARE	THR A:134 , ASP A:135 , LYS A:159 , HOH A:1188	BINDING SITE FOR RESIDUE SO4 A 1007
7	AC7	SOFTWARE	ILE A:45 , LYS A:175 , THR A:242 , HOH A:1126 , HOH A:1162	BINDING SITE FOR RESIDUE SO4 A 1008
8	AC8	SOFTWARE	LEU A:39 , CYS A:40 , HIS A:57 , ASP A:189 , ALA A:190 , CYS A:191 , LYS A:192 , GLY A:193 , ASP A:194 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:218 , CYS A:219 , GLY A:226 , HOH A:1143	BINDING SITE FOR RESIDUE 412 A 1001

Asymmetric/Biological Unit

No.	Residues
1	A:40	-	A:58
2	A:136	-	A:201
3	A:168	-	A:182
4	A:191	-	A:219

Asymmetric/Biological Unit

No.	Residues
1	Ser A:37	-	Pro A:37A

Asymmetric/Biological Unit (25, 25)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_011778	W	399	R	FA11_HUMAN	Polymorphism	1800439	A	W	27	R
02	UniProt	VAR_067945	W	401	R	FA11_HUMAN	Disease (FA11D)	281875262	A	W	29	R
03	UniProt	VAR_067946	V	403	M	FA11_HUMAN	Disease (FA11D)	281875266	A	V	31	M
04	UniProt	VAR_012092	T	404	N	FA11_HUMAN	Disease (FA11D)	121965067	A	T	32	N
05	UniProt	VAR_054901	G	418	V	FA11_HUMAN	Disease (FA11D)	121965071	A	G	42	V
06	UniProt	VAR_012093	A	430	V	FA11_HUMAN	Disease (FA11D)	121965068	A	A	56	V
07	UniProt	VAR_067947	I	454	K	FA11_HUMAN	Disease (FA11D)	281875241	A	I	77	K
08	UniProt	VAR_012094	F	460	V	FA11_HUMAN	Disease (FA11D)	121965065	A	F	82	V
09	UniProt	VAR_067948	I	481	S	FA11_HUMAN	Disease (FA11D)	281875242	A	I	103	S
10	UniProt	VAR_012095	T	493	I	FA11_HUMAN	Disease (FA11D)	---	A	A	115	I
11	UniProt	VAR_067949	S	503	P	FA11_HUMAN	Disease (FA11D)	140068026	A	S	126	P
12	UniProt	VAR_067950	D	506	G	FA11_HUMAN	Disease (FA11D)	281875258	A	D	129	G
13	UniProt	VAR_054902	Y	511	H	FA11_HUMAN	Disease (FA11D)	281875278	A	Y	133	H
14	UniProt	VAR_067951	C	514	F	FA11_HUMAN	Disease (FA11D)	281875249	A	C	136	F
15	UniProt	VAR_067952	D	526	E	FA11_HUMAN	Disease (FA11D)	281875263	A	D	148	E
16	UniProt	VAR_054903	P	538	L	FA11_HUMAN	Disease (FA11D)	139695003	A	P	161	L
17	UniProt	VAR_076518	E	543	K	FA11_HUMAN	Disease (FA11D)	142952627	A	E	166	K
18	UniProt	VAR_076519	H	552	R	FA11_HUMAN	Disease (FA11D)	369935706	A	H	174	R
19	UniProt	VAR_054904	E	565	K	FA11_HUMAN	Disease (FA11D)	281875275	A	E	186	K
20	UniProt	VAR_067953	S	575	L	FA11_HUMAN	Disease (FA11D)	281875250	A	S	195	L
21	UniProt	VAR_054905	W	587	S	FA11_HUMAN	Disease (FA11D)	121965072	A	W	203	S
22	UniProt	VAR_012096	S	594	R	FA11_HUMAN	Disease (FA11D)	28934609	A	S	214	R
23	UniProt	VAR_067954	E	597	K	FA11_HUMAN	Disease (FA11D)	281875251	A	E	217	K
24	UniProt	VAR_067955	Y	608	H	FA11_HUMAN	Disease (FA11D)	281875255	A	Y	228	H
25	UniProt	VAR_054906	I	618	S	FA11_HUMAN	Disease (FA11D)	281875276	A	I	238	S

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	FA11_HUMAN	388-623	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	FA11_HUMAN	427-432	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	FA11_HUMAN	569-580	1	A:189-198B

(no "Exon" information available for 1ZML)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:237
 aligned with FA11_HUMAN | P03951 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:237
                                   397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       
          FA11_HUMAN    388 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQA  624
               SCOP domains d1zmla_ A: Coagulation factor XI                                                                                                                                                                                                              SCOP domains
               CATH domains 1zmlA01     1zmlA02 A:28-121,A:234-244 Trypsin-like serine proteases                                           1zmlA01 A:16-27,A:122-233 Trypsin-like serine proteases                                                            1zmlA02     CATH domains
               Pfam domains Trypsin-1zmlA01 A:16-238                                                                                                                                                                                                               ------ Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh...hhh.eeee....hhhhh......eeeeeeee.....hhhhh...eeeee................hhhhhh...eeeeeee..............eeee..eehhhhhhhhh........eeee................eeeee....eeeeeeeee..........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------R-R-MN-------------V-----------V-----------------------K-----V--------------------S-----------I---------P--G----H--F-----------E-----------L----K--------R------------K---------L-----------S------R--K----------H---------S------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 388-623                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zml A   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIAEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQA  244
                                    25        35  ||||  41      ||53      ||60        70        80 |      89        99       109       119|      130  |    139       149|      160       170   |   179     | 188|      197 ||| ||203||     217       227       237       
                                                37A|||         48|      59A||                    81A                                   119|        132A              149|                   173A        184A 188A       198A|| |||| ||                                   
                                                 37B||          51       59B|                                                           121                           151                                                198B| |||| ||                                   
                                                  37C|                    59C                                                                                                                                              201 |||| ||                                   
                                                   37D                                                                                                                                                                      202A||| ||                                   
                                                                                                                                                                                                                             202B|| ||                                   
                                                                                                                                                                                                                              202C| ||                                   
                                                                                                                                                                                                                               202D ||                                   
                                                                                                                                                                                                                                  204|                                   
                                                                                                                                                                                                                                   209

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/Biological 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: Eukaryotic proteases (1343)

Protein domain: Coagulation factor XI (26)

Human (Homo sapiens) [TaxId: 9606] (26)

d1zmla_

Asymmetric/Biological 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	1zmlA02	A:28-121,A:234-244
1b	1zmlA01	A:16-27,A:122-233

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

Trypsin-1zmlA01

A:16-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FA11_HUMAN | P03951)

molecular function
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	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: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:0070009	serine-type aminopeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the N-terminus of 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: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:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0007597	blood coagulation, intrinsic pathway	A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0031639	plasminogen activation	The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide.
	GO:0051919	positive regulation of fibrinolysis	Any process that activates, maintains or increases the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0030193	regulation of blood coagulation	Any process that modulates the frequency, rate or extent of blood coagulation.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:37 - Pro A:37A	[ RasMol ]

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Ligands, Modified Residues, Ions (3, 8)

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SS Bonds (4, 4)

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