Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE FXIA CATALYTIC DOMAIN IN COMPLEX WITH ECOTIN MUTANT (ECOTINP)
 
Authors :  L. Jin, P. Pandey, R. E. Babine, J. C. Gorga, K. J. Seidl, E. Gelfand, D. T. Weaver, S. S. Abdel-Meguid, J. E. Strickler
Date :  04 Nov 04  (Deposition) - 16 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fxia; Catalytic Domain; Serine Protease; Ecotin; Substrate- Like Interaction, Blood Clotting/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Jin, P. Pandey, R. E. Babine, J. C. Gorga, K. J. Seidl, E. Gelfand, D. T. Weaver, S. S. Abdel-Meguid, J. E. Strickler
Crystal Structures Of The Fxia Catalytic Domain In Complex With Ecotin Mutants Reveal Substrate-Like Interactions
J. Biol. Chem. V. 280 4704 2005
PubMed-ID: 15545266  |  Reference-DOI: 10.1074/JBC.M411309200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR XI
    ChainsA, B
    EC Number3.4.21.27
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    FragmentCATALYTIC DOMAIN
    GeneF11
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPLASMA THROMBOPLASTIN ANTECEDENT;
PTA;
FXI
 
Molecule 2 - ECOTIN
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneECO,ETI
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:160 , ALA B:183 , ASP B:189 , TYR B:228BINDING SITE FOR RESIDUE NA B 1001
2AC2SOFTWARETRP B:137 , THR B:139 , PRO B:198 , SER B:198BBINDING SITE FOR RESIDUE NA B 1002

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:219
5B:40 -B:58
6B:136 -B:201
7B:168 -B:182
8B:191 -B:219
9C:50 -C:87
10D:50 -D:87

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:37 -Pro A:37A
2Ser B:37 -Pro B:37A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (25, 50)

Asymmetric/Biological Unit (25, 50)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_011778W399RFA11_HUMANPolymorphism1800439A/BW27R
02UniProtVAR_067945W401RFA11_HUMANDisease (FA11D)281875262A/BW29R
03UniProtVAR_067946V403MFA11_HUMANDisease (FA11D)281875266A/BV31M
04UniProtVAR_012092T404NFA11_HUMANDisease (FA11D)121965067A/BT32N
05UniProtVAR_054901G418VFA11_HUMANDisease (FA11D)121965071A/BG42V
06UniProtVAR_012093A430VFA11_HUMANDisease (FA11D)121965068A/BA56V
07UniProtVAR_067947I454KFA11_HUMANDisease (FA11D)281875241A/BI77K
08UniProtVAR_012094F460VFA11_HUMANDisease (FA11D)121965065A/BF82V
09UniProtVAR_067948I481SFA11_HUMANDisease (FA11D)281875242A/BI103S
10UniProtVAR_012095T493IFA11_HUMANDisease (FA11D)  ---A/BA115I
11UniProtVAR_067949S503PFA11_HUMANDisease (FA11D)140068026A/BS126P
12UniProtVAR_067950D506GFA11_HUMANDisease (FA11D)281875258A/BD129G
13UniProtVAR_054902Y511HFA11_HUMANDisease (FA11D)281875278A/BY133H
14UniProtVAR_067951C514FFA11_HUMANDisease (FA11D)281875249A/BC136F
15UniProtVAR_067952D526EFA11_HUMANDisease (FA11D)281875263A
B
D148
149
E
16UniProtVAR_054903P538LFA11_HUMANDisease (FA11D)139695003A/BP161L
17UniProtVAR_076518E543KFA11_HUMANDisease (FA11D)142952627A/BE166K
18UniProtVAR_076519H552RFA11_HUMANDisease (FA11D)369935706A/BH174R
19UniProtVAR_054904E565KFA11_HUMANDisease (FA11D)281875275A/BE186K
20UniProtVAR_067953S575LFA11_HUMANDisease (FA11D)281875250A/BS195L
21UniProtVAR_054905W587SFA11_HUMANDisease (FA11D)121965072A/BW203S
22UniProtVAR_012096S594RFA11_HUMANDisease (FA11D)28934609A/BS214R
23UniProtVAR_067954E597KFA11_HUMANDisease (FA11D)281875251A/BE217K
24UniProtVAR_067955Y608HFA11_HUMANDisease (FA11D)281875255A/BY228H
25UniProtVAR_054906I618SFA11_HUMANDisease (FA11D)281875276A/BI238S

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.FA11_HUMAN388-623
 
  2A:16-243
B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.FA11_HUMAN427-432
 
  2A:53-58
B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.FA11_HUMAN569-580
 
  2A:189-198B
B:189-198B

(-) Exons   (0, 0)

(no "Exon" information available for 1XXF)

(-) Sequences/Alignments

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
(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: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 d1xxfa_ A: Coagulation factor XI                                                                                                                                                                                                              SCOP domains
               CATH domains 1xxfA01     1xxfA02 A:28-121,A:234-244 Trypsin-like serine proteases                                           1xxfA01 A:16-27,A:122-233 Trypsin-like serine proteases                                                            1xxfA02     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee...eeeeeeeeeee..eeee.hhhhh...hhh.eeeee...hhhhh......eeeeeeee.............eeeee................hhhhhhh....eeeee..............eeee..eehhhhhhhhh........eeee................eeeeee..eeeeeeeeeee.........eeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------R-R-MN-------------V-----------V-----------------------K-----V--------------------S-----------I---------P--G----H--F-----------------------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
                1xxf A   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQA  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                                   

Chain B 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 d1xxfb_ B: Coagulation factor XI                                                                                                                                                                                                              SCOP domains
               CATH domains 1xxfB01     1xxfB02 B:28-121,B:234-244 Trypsin-like serine proteases                                           1xxfB01 B:16-27,B:122-233 Trypsin-like serine proteases                                                            1xxfB02     CATH domains
           Pfam domains (1) Trypsin-1xxfB01 B:16-238                                                                                                                                                                                                               ------ Pfam domains (1)
           Pfam domains (2) Trypsin-1xxfB02 B:16-238                                                                                                                                                                                                               ------ Pfam domains (2)
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh...hhh.eeee....hhhhh......eeeeeeee.....hhhhh...eeeee................hhhhh......eeeee..............eeee..eehhhhhhhh.........eeee................eeeee....eeeeeeeeee.........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: B:16-243 UniProt: 388-623                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xxf B   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQA  244
                                    25        35  ||||  41      ||53      ||60        70        80 |      89        99       109       119|      130  |    139      |150       160       170   |   179     | 188|      197 ||| ||203||     217       227       237       
                                                37A|||         48|      59A||                    81A                                   119|        132A           146|                      173A        184A 188A       198A|| |||| ||                                   
                                                 37B||          51       59B|                                                           121                        148                                                   198B| |||| ||                                   
                                                  37C|                    59C                                                                                                                                              201 |||| ||                                   
                                                   37D                                                                                                                                                                      202A||| ||                                   
                                                                                                                                                                                                                             202B|| ||                                   
                                                                                                                                                                                                                              202C| ||                                   
                                                                                                                                                                                                                               202D ||                                   
                                                                                                                                                                                                                                  204|                                   
                                                                                                                                                                                                                                   209                                   

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:138
                                    34        44        54        64        74        84        94       104       114       124       134       144       154        
          ECOT_ECOLI     25 QPLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMACPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  162
               SCOP domains d1xxfc_ C: Ecotin, trypsin inhibitor                                                                                                       SCOP domains
               CATH domains 1xxfC00 C:5-142  [code=2.60.40.550, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.........eeeeee......hhh.eeeeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeeeee.........eeeeee..hhhh.eee......eeeeee...eeeeeeeee....ee.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1xxf C    5 QPLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPDFTRVVCPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134        

Chain D from PDB  Type:PROTEIN  Length:138
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:138
                                    34        44        54        64        74        84        94       104       114       124       134       144       154        
          ECOT_ECOLI     25 QPLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMACPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  162
               SCOP domains d1xxfd_ D: Ecotin, trypsin inhibitor                                                                                                       SCOP domains
               CATH domains 1xxfD00 D:5-142  [code=2.60.40.550, no name defined]                                                                                       CATH domains
           Pfam domains (1) --Ecotin-1xxfD01 D:7-133                                                                                                         --------- Pfam domains (1)
           Pfam domains (2) --Ecotin-1xxfD02 D:7-133                                                                                                         --------- Pfam domains (2)
         Sec.struct. author .hhhhh.........eeeeee......hhh.eeeeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeeeee.........eeeeee..hhhh.eee......eeeeee...eeeeeeeee....ee.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1xxf D    5 QPLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPDFTRVVCPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134        

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (25, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

Chain C,D   (ECOT_ECOLI | P23827)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:37 - Pro A:37A  [ RasMol ]  
    Ser B:37 - Pro B:37A  [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1xxf
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ECOT_ECOLI | P23827
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  FA11_HUMAN | P03951
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.27
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  612416
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ECOT_ECOLI | P23827
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  FA11_HUMAN | P03951
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ECOT_ECOLI | P238271azz 1ecy 1ecz 1ezs 1ezu 1fi8 1id5 1ifg 1n8o 1p0s 1slu 1slv 1slw 1slx 1xx9 1xxd 4iw4 4niy
        FA11_HUMAN | P039511xx9 1xxd 1zhm 1zhp 1zhr 1zjd 1zlr 1zmj 1zml 1zmn 1zom 1zpb 1zpc 1zpz 1zrk 1zsj 1zsk 1zsl 1ztj 1ztk 1ztl 2f83 2fda 2j8j 2j8l 3bg8 3sor 3sos 4cr5 4cr9 4cra 4crb 4crc 4crd 4cre 4crf 4crg 4d76 4d7f 4d7g 4na7 4na8 4ty6 4ty7 4wxi 4x6m 4x6n 4x6o 4x6p 4y8x 4y8y 4y8z 5e2o 5e2p 5eod 5eok 5exl 5exm 5exn 5i25 5q0d 5q0e 5q0f 5q0g 5q0h 5tks 5tkt 5tku

(-) Related Entries Specified in the PDB File

1xx9 1xxd