Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF RECOMBINANT GLA-DOMAINLESS PROTHROMBIN MUTANT S525A
 
Authors :  N. Pozzi, W. Niu, D. W. Gohara, Z. Chen, E. Di Cera
Date :  15 Nov 12  (Deposition) - 26 Jun 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Prothrombin, Kringle, Serine Protease, Coagulation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Pozzi, Z. Chen, D. W. Gohara, W. Niu, T. Heyduk, E. Di Cera
Crystal Structure Of Prothrombin Reveals Conformational Flexibility And Mechanism Of Activation.
J. Biol. Chem. V. 288 22734 2013
PubMed-ID: 23775088  |  Reference-DOI: 10.1074/JBC.M113.466946
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTHROMBIN
    Chains: A, B
    EC Number: 3.4.21.5
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: BHK CELL
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 90-622
    Gene: F2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN HEAVY CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:373BINDING SITE FOR RESIDUE NAG A 701
2AC2SOFTWAREASN B:373BINDING SITE FOR RESIDUE NAG B 701
3AC3SOFTWAREARG B:92 , ASN B:100 , THR B:102 , THR B:103BINDING SITE FOR RESIDUE NAG B 702
4AC4SOFTWAREHIS B:76 , ASN B:78 , GLU B:85BINDING SITE FOR RESIDUE NAG B 703

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:170 -A:248
2A:191 -A:231
3A:219 -A:243
4A:293 -A:439
5A:348 -A:364
6A:493 -A:507
7A:521 -A:551
8B:86 -B:126
9B:114 -B:138
10B:170 -B:248
11B:191 -B:231
12B:219 -B:243
13B:293 -B:439
14B:348 -B:364
15B:493 -B:507
16B:521 -B:551

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:342 -Pro A:343
2Tyr B:93 -Pro B:94
3Ser B:342 -Pro B:343

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HZH)

(-) Sequences/Alignments

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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee...hhhhhh............................eeee......eee....................hhhhhh.hhhhh...............................ee........eeeeee....eeeeeeee....eeeehhhh.ee....ee.hhh.eeeee...............eeeeeeee..............eeeee................hhhhhhhhhhhh..eee...hhhhhhh............ee.ee...hhhhhhhhh.......eeee...................eeeee......eeeeeee............eeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hzh A 169 QCVPDRGQQYQGRLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDFGYCDLNYCEEAVEETSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE 579
                                   178       188       198       208       218       228       238       248     ||277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577  
                                                                                                               254|                                                                                                                                                                                                                                                                                                                 
                                                                                                                274                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........................................................eeeee..eeee..........hhhhh.....................................................eeee.....eeee...........................hhhhh..............hhhhhhh....................eeeeee.....eeeeeee....eeee.....ee....ee.hhh.eeeee.............eee.eeeeee..............eeeee................hhhhhhhh.....eeeee......................eeeee..hhhhhhhhh.......ee.....................eeeee......eeeeeee..............eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hzh B  68 GLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHPGADLQENFCRNPDSSTTGPWCYTTDPTVRRQECSIPVCQCVPDRGQQYQGRLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDFGYCDLNYCEEAVEETSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE 579
                                    77        87        97       107       117       127       137     ||172       182       192       202       212       222       232       242       252 ||    281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571        
                                                                                                     143|                                                                                  254|                                                                                                                                                                                                                                                                                                                 
                                                                                                      169                                                                                   274
   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 4HZH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (51, 51)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:342 - Pro A:343   [ RasMol ]  
    Ser B:342 - Pro B:343   [ RasMol ]  
    Tyr B:93 - Pro B:94   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4hzh
    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
  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
  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
        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 4i7y 4loy 4lxb 4lz1 4lz4 4mlf 4n3l 4nze 4nzq 4o03 4rkj 4rko 4rn6 4thn 4ud9 4udw 4ue7 4ueh 4ufd 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

3nxp CRYSTAL STRUCTURE OF HUMAN PRETHROMBIN-1
4hzq