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 :  THROMBIN IN COMPLEX WITH 4-(((1-((2S)-1-((2R)-2-( BENZYLSULFONYLAMINO)-3-PHENYL-PROPANOYL)PYRROLIDIN-2-YL)-1-OXO-ETHYL)AMINO)METHYL)BENZAMIDINE
 
Authors :  E. Ruehmann, A. Heine, G. Klebe
Date :  16 Mar 15  (Deposition) - 27 Jan 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  H,I,L
Keywords :  Hydrolase, Hydrolase Inhibitor Complex, Serine Protease, Blood Coagulation, Blood Clotting, Convertion Of Fibrinogen To Fibrin, Blood Clotting Inhibitor, Thrombin Inhibitor, Preorganization, Glycosylation, Blood (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. H. Ruhmann, M. Rupp, M. Betz, A. Heine, G. Klebe
Boosting Affinity By Correct Ligand Preorganization For The S2 Pocket Of Thrombin: A Study By Isothermal Titration Calorimetry, Molecular Dynamics, And High-Resolution Crystal Structures.
Chemmedchem V. 11 309 2016
PubMed-ID: 26762840  |  Reference-DOI: 10.1002/CMDC.201500531

(-) Compounds

Molecule 1 - THROMBIN LIGHT CHAIN
    Chains: L
    EC Number: 3.4.21.5
    Fragment: RESIDUES 333-361
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PURIFIED FROM HUMAN BLOOD PLASMA
 
Molecule 2 - THROMBIN HEAVY CHAIN
    Chains: H
    EC Number: 3.4.21.5
    Fragment: RESIDUES 364-621
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PURIFIED FROM HUMAN BLOOD PLASMA
 
Molecule 3 - HIRUDIN VARIANT-2
    Chains: I
    Fragment: RESIDUES 61-72
    Organism Common: MEDICINAL LEECH
    Organism Scientific: HIRUDO MEDICINALIS
    Organism Taxid: 6421
    Other Details: HIRUDIN (54-65) (SULFATED)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HIL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA2Ligand/IonSODIUM ION
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PO41Ligand/IonPHOSPHATE ION
5S491Ligand/Ion(2S)-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]-1-[(2R)-3-PHENYL-2-[(PHENYLMETHYL)SULFONYLAMINO]PROPANOYL]PYRROLIDINE-2-CARBOXAMIDE
6TYS1Mod. Amino AcidO-SULFO-L-TYROSINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS H:169 , THR H:172 , PHE H:204A , HOH H:2203 , HOH H:2204 , HOH H:2209BINDING SITE FOR RESIDUE NA H1247
2AC2SOFTWAREARG H:221A , LYS H:224 , HOH H:2225 , HOH H:2226 , HOH H:2236 , HOH H:2257BINDING SITE FOR RESIDUE NA H1248
3AC3SOFTWAREARG H:93 , ASN H:95 , PO4 H:1252 , HOH H:2117 , HOH H:2123BINDING SITE FOR RESIDUE GOL H1249
4AC4SOFTWAREARG H:173 , HOH H:2210 , ILE L:14K , HOH L:2027BINDING SITE FOR RESIDUE GOL H1250
5AC5SOFTWAREHIS H:57 , TYR H:60A , TRP H:60D , GLU H:97A , ASP H:189 , ALA H:190 , GLU H:192 , SER H:195 , VAL H:213 , SER H:214 , TRP H:215 , GLY H:216 , GLY H:219 , CYS H:220 , GLY H:226 , HOH H:2252 , HOH H:2275BINDING SITE FOR RESIDUE S49 H1251
6AC6SOFTWAREASN H:95 , ASP H:100 , ARG H:101 , ARG H:175 , GOL H:1249 , HOH H:2120 , HOH H:2215 , HOH H:2216BINDING SITE FOR RESIDUE PO4 H1252
7AC7SOFTWAREASN H:60G , HOH H:2279BINDING SITE FOR MONO-SACCHARIDE NAG H1060 BOUND TO ASN H 60G

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:42 -H:58
2H:122 -L:1
3H:168 -H:182
4H:191 -H:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser H:36A-Pro H:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UFD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UFD)

(-) Exons   (0, 0)

(no "Exon" information available for 4UFD)

(-) 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 H from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeeee....eeeehhhh.eehhhhee.hhh.eeeee.............eeeeeeeeee..............eeeee................hhhhhhhhh....eeeeee.............eeeeee..hhhhhhhh........eeee...................eeeee......eeeeeeeee..........eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ufd H   16 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG  246
                                    25        35 |      44        54      |60D|||||   65        75  |     84        94   |   103       113       123      |130       140      |152       162       172       182  |  ||187       197       205       215 ||  | 225       235       245 
                                               36A                      60A||||||||               77A                  97A                             129A||               147|                               184A  ||||               204A|          217|  |                         
                                                                         60B|||||||                                                                     129B|                150                                  186A|||                204B           219  |                         
                                                                          60C||||||                                                                      129C                                                      186B||                                 221A                         
                                                                           60D|||||                                                                                                                                 186C|                                                              
                                                                            60E||||                                                                                                                                  186D                                                              
                                                                             60F|||                                                                                                                                                                                                    
                                                                              60G||                                                                                                                                                                                                    
                                                                               60H|                                                                                                                                                                                                    
                                                                                60I                                                                                                                                                                                                    


Chain I from PDB  Type:PROTEIN  Length:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                4ufd I  562 EyLQ  565
                             |  
                           563-TYS


Chain L from PDB  Type:PROTEIN  Length:27
                                                            
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author ........hhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                4ufd L   1B ADCGLRPLFEKKSLEDKTERELLESYI  14K
                            ||       8      |14D|||||||
                           1B|            14A||||||14J|
                            1A             14B||||||14K
                                            14C||||||  
                                             14D|||||  
                                              14E||||  
                                               14F|||  
                                                14G||  
                                                 14H|  
                                                  14I
   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  (0, 0)

(no "SCOP Domain" information available for 4UFD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UFD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UFD)

(-) Gene Ontology  (56, 57)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    S49  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TYS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser H:36A - Pro H:37   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ufd
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HIRV2_HIRME | P09945
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  THRB_HUMAN | P00734
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.5
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  HIRV2_HIRME | P09945
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  THRB_HUMAN | P00734
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HIRV2_HIRME | P09945: 1a2c 1a46 1a4w 1a5g 1a61 1b5g 1doj 1hgt 1k21 1k22 1nrs 1tbz 1tmb 1tmu 1vzq 1w7g 1way 1wbg 2bvr 2bvs 2bvx 2bxt 2bxu 2c8w 2c8x 2c8y 2c8z 2c90 2c93 2r2m 2zfq 2zfr 2zg0 2zhe 2zhf 2zhw 3biu 3biv 3f68 3hat 3htc 3p17 3qto 3qtv 3qwc 3qx5 3rlw 3rly 3rm0 3rm2 3rml 3rmm 3rmn 3rmo 3sha 3shc 3si3 3si4 3sv2 3t5f 3tu7 3u98 3u9a 3uwj 4bao 4e7r 4htc 4loy 4n3l 4nze 4ud9 4udw 4ue7 4ueh 4ufe 4uff 4ufg 5a2m 5af9 5jfd 5jzy
        THRB_HUMAN | P00734: 1a2c 1a3b 1a3e 1a46 1a4w 1a5g 1a61 1abi 1abj 1ad8 1ae8 1afe 1aht 1ai8 1aix 1awf 1awh 1ay6 1b5g 1b7x 1ba8 1bb0 1bcu 1bhx 1bmm 1bmn 1bth 1c1u 1c1v 1c1w 1c4u 1c4v 1c4y 1c5l 1c5n 1c5o 1ca8 1d3d 1d3p 1d3q 1d3t 1d4p 1d6w 1d9i 1de7 1dit 1dm4 1doj 1dwb 1dwc 1dwd 1dwe 1dx5 1e0f 1eb1 1eoj 1eol 1fpc 1fph 1g30 1g32 1g37 1ghv 1ghw 1ghx 1ghy 1gj4 1gj5 1h8d 1h8i 1hag 1hah 1hai 1hao 1hap 1hbt 1hdt 1hgt 1hlt 1hut 1hxe 1hxf 1ihs 1iht 1jmo 1jou 1jwt 1k21 1k22 1kts 1ktt 1lhc 1lhd 1lhe 1lhf 1lhg 1mh0 1mu6 1mu8 1mue 1nm6 1no9 1nrn 1nro 1nrp 1nrq 1nrr 1nrs 1nt1 1nu7 1nu9 1ny2 1nzq 1o0d 1o2g 1o5g 1ook 1oyt 1p8v 1ppb 1qbv 1qhr 1qj1 1qj6 1qj7 1qur 1rd3 1riw 1sb1 1sfq 1sg8 1sgi 1shh 1sl3 1sr5 1t4u 1t4v 1ta2 1ta6 1tb6 1tbz 1thp 1thr 1ths 1tmb 1tmt 1tmu 1tom 1tq0 1tq7 1twx 1uma 1uvs 1vr1 1vzq 1w7g 1way 1wbg 1xm1 1xmn 1ype 1ypg 1ypj 1ypk 1ypl 1ypm 1z71 1z8i 1z8j 1zgi 1zgv 1zrb 2a0q 2a2x 2a45 2afq 2ank 2anm 2b5t 2bdy 2bvr 2bvs 2bvx 2bxt 2bxu 2c8w 2c8x 2c8y 2c8z 2c90 2c93 2cf8 2cf9 2cn0 2feq 2fes 2gde 2gp9 2h9t 2hgt 2hnt 2hpp 2hpq 2hwl 2jh0 2jh5 2jh6 2od3 2pgb 2pgq 2pks 2pw8 2r2m 2thf 2uuf 2uuj 2uuk 2v3h 2v3o 2zc9 2zda 2zdv 2zf0 2zff 2zfp 2zfq 2zfr 2zg0 2zgb 2zgx 2zhe 2zhf 2zhq 2zhw 2zi2 2ziq 2znk 2zo3 3b23 3b9f 3bef 3bei 3bf6 3biu 3biv 3bv9 3c1k 3c27 3d49 3da9 3dd2 3dhk 3dt0 3dux 3e6p 3ee0 3egk 3eq0 3f68 3gic 3gis 3hat 3hkj 3htc 3jz1 3jz2 3k65 3ldx 3lu9 3nxp 3p17 3p6z 3p70 3pmh 3po1 3qdz 3qgn 3qlp 3qto 3qtv 3qwc 3qx5 3r3g 3rlw 3rly 3rm0 3rm2 3rml 3rmm 3rmn 3rmo 3s7h 3s7k 3sha 3shc 3si3 3si4 3sqe 3sqh 3sv2 3t5f 3tu7 3u69 3u8o 3u8r 3u8t 3u98 3u9a 3utu 3uwj 3vxe 3vxf 4ax9 4ayv 4ayy 4az2 4bah 4bak 4bam 4ban 4bao 4baq 4boh 4ch2 4ch8 4dih 4dii 4dt7 4dy7 4e05 4e06 4e7r 4h6s 4h6t 4hfp 4htc 4hzh 4i7y 4loy 4lxb 4lz1 4lz4 4mlf 4n3l 4nze 4nzq 4o03 4rkj 4rko 4rn6 4thn 4ud9 4udw 4ue7 4ueh 4ufe 4uff 4ufg 4yes 5a2m 5af9 5afy 5afz 5ahg 5cmx 5do4 5e8e 5edk 5edm 5ew1 5ew2 5gds 5gim 5jdu 5jfd 5jzy 5l6n 5luw 5luy 5nhu 5to3 7kme 8kme

(-) Related Entries Specified in the PDB File

4ufe THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N -(2-((4-CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-OXO-BUTYL)-3 -PHENYL-PROPANAMIDE
4uff THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N -(2-((4-CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-OXO-ETHYL)-N -METHYL-3-PHENYL-PROPANAMIDE
4ufg THROMBIN IN COMPLEX WITH (2R)-2-(BENZYLSULFONYLAMINO)-N -((1S)-2-((4-CARBAMIMIDOYLPHENYL)METHYLAMINO)-1-METHYL- 2-OXO-ETHYL)-N-METHYL-3-PHENYL-PROPANAMIDE ETHANE