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(-) Description

Title :  RUBIDIUM SITES IN BLOOD COAGULATION FACTOR VIIA
 
Authors :  K. Vadivel, A. Schmidt, D. Cascio, K. Padmanabhan, S. P. Bajaj
Date :  08 Dec 12  (Deposition) - 16 Apr 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  H,L,T
Keywords :  Serine Protease, Hydrolase, Tissue Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Vadivel, A. Schmidt, D. Cascio, K. Padmanabhan, S. P. Bajaj
Sodium Site In Blood Coagulation Factor Viia: Absence Of Occupancy By Rubidium
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COAGULATION FACTOR VII
    Chains: L
    EC Number: 3.4.21.21
    Engineered: YES
    Fragment: LIGHT CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synonym: PROCONVERTIN, SERUM PROTHROMBIN CONVERSION ACCELERATOR, SPCA, FACTOR VII LIGHT CHAIN, FACTOR VII HEAVY CHAIN
    Synthetic: YES
 
Molecule 2 - COAGULATION FACTOR VII
    Chains: H
    EC Number: 3.4.21.21
    Engineered: YES
    Fragment: HEAVY CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synonym: PROCONVERTIN, SERUM PROTHROMBIN CONVERSION ACCELERATOR, SPCA, FACTOR VII LIGHT CHAIN, FACTOR VII HEAVY CHAIN
    Synthetic: YES
 
Molecule 3 - TISSUE FACTOR
    Chains: T
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synonym: TF, COAGULATION FACTOR III, THROMBOPLASTIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 30)

Asymmetric/Biological Unit (8, 30)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2BGC1Ligand/IonBETA-D-GLUCOSE
3CA4Ligand/IonCALCIUM ION
4CGU10Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
5CL4Ligand/IonCHLORIDE ION
6FUC1Ligand/IonALPHA-L-FUCOSE
7MG3Ligand/IonMAGNESIUM ION
8RB6Ligand/IonRUBIDIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN L:49 , SER L:52 , PRO L:54 , TYR L:68BINDING SITE FOR RESIDUE BGC L 201
02AC2SOFTWAREGLY L:58 , SER L:60 , ARG T:131BINDING SITE FOR RESIDUE FUC L 202
03AC3SOFTWARECGU L:25 , CGU L:29 , HOH L:338 , HOH L:339BINDING SITE FOR RESIDUE MG L 203
04AC4SOFTWARECGU L:26 , CGU L:29 , RB L:205 , HOH L:342 , HOH L:344 , HOH L:422BINDING SITE FOR RESIDUE CA L 204
05AC5SOFTWARECGU L:26 , CGU L:29 , CA L:204 , HOH L:343 , HOH L:344 , HOH L:423BINDING SITE FOR RESIDUE RB L 205
06AC6SOFTWARECGU L:16 , CGU L:26 , HOH L:345 , HOH L:346BINDING SITE FOR RESIDUE MG L 206
07AC7SOFTWARECGU L:7 , CGU L:16 , CGU L:20 , HOH L:427 , HOH L:428 , HOH L:429BINDING SITE FOR RESIDUE RB L 207
08AC8SOFTWARECGU L:6 , CGU L:20 , HOH L:402 , HOH L:403 , HOH L:404BINDING SITE FOR RESIDUE CA L 208
09AC9SOFTWARECGU L:14 , CGU L:19 , HOH L:405 , HOH L:406BINDING SITE FOR RESIDUE MG L 209
10BC1SOFTWAREASP L:46 , GLY L:47 , GLN L:49 , ASP L:63 , GLN L:64 , HOH L:336 , HOH T:428BINDING SITE FOR RESIDUE CA L 210
11BC2SOFTWARECGU L:16 , CGU L:20 , GLN L:21 , CGU L:26BINDING SITE FOR RESIDUE RB L 211
12BC3SOFTWARECYS L:114 , HIS L:115 , TYR L:118BINDING SITE FOR RESIDUE RB L 212
13BC4SOFTWAREASP H:189 , SER H:190 , LYS H:192 , SER H:195 , SER H:214 , TRP H:215 , GLY H:216 , GLY H:219 , GLY H:226 , HOH H:414BINDING SITE FOR RESIDUE BEN H 301
14BC5SOFTWAREGLU H:70 , ASP H:72 , GLU H:75 , GLU H:80 , HOH H:429 , HOH H:469BINDING SITE FOR RESIDUE CA H 302
15BC6SOFTWAREARG H:84BINDING SITE FOR RESIDUE CL H 303
16BC7SOFTWAREASP H:146 , CYS H:220 , THR H:221 , ALA H:221A , THR T:53 , HOH T:451BINDING SITE FOR RESIDUE RB H 304
17BC8SOFTWARESER H:170H , PRO H:170IBINDING SITE FOR RESIDUE RB H 305
18BC9SOFTWAREARG H:162 , SER H:232 , HOH H:417 , HOH H:545BINDING SITE FOR RESIDUE CL H 306
19CC1SOFTWAREASN H:37 , LYS H:60C , ASN H:60DBINDING SITE FOR RESIDUE CL H 307
20CC2SOFTWAREGLU T:130 , ARG T:144 , TYR T:153 , ASN T:173BINDING SITE FOR RESIDUE CL T 301

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:27
2H:42 -H:58
3H:168 -H:182
4H:191 -H:220
5L:17 -L:22
6L:50 -L:61
7L:55 -L:70
8L:72 -L:81
9L:91 -L:102
10L:98 -L:112
11L:114 -L:127
12L:135 -H:122
13T:49 -T:57
14T:186 -T:209

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe H:256 -Pro H:257
2Glu T:26 -Pro T:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IBL)

(-) 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:254
                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeee....eeeehhhhhh...hhh.eeeee............eeeeeeeeeee............eeeee................hhhhhhhhhhhh.eeeeee..............eeeeeeeehhhhhhhh.............eeee.........hhhhh..eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh.......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ibl H   16 IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP  257
                                    25        35|       46        56    ||||62        72        82        92       102       112       122      129C|||||  139       150       160       170|||||||175       184   |   193       203       213   || |223       233       243       253    
                                              35|                     60A|||                                                                  129A|||||||          147|                  170A||||||175     184A 188A                           217| |                                     
                                               37                      60B||                                                                   129B||||||           149                   170B|||||||                                           219 |                                     
                                                                        60C|                                                                    129C|||||                                  170C||||||                                            221A                                     
                                                                         60D                                                                     129D||||                                   170D|||||                                                                                     
                                                                                                                                                  129E|||                                    170E||||                                                                                     
                                                                                                                                                   129F||                                     170F|||                                                                                     
                                                                                                                                                    129G|                                      170G||                                                                                     
                                                                                                                                                      134                                       170H|                                                                                     
                                                                                                                                                                                                 170I                                                                                     


Chain L from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..............eeeee..eeeee....ee.....ee.hhh....hhhhhh..eeeee..eeeeee....eee......eee........hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ibl L    3 AFLeeLRPGSLeReCKeeQCSFeeAReIFKDAeRTKLFWISYSDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILE  142
                               ||   12 | |  ||22  ||  | 32  |     42        52        62        72        82        92       102       112       122       132       142
                               6-CGU  14-CGU||    ||  |     |                                                                                                           
                                7-CGU   16-CGU    ||  |     |                                                                                                           
                                           19-CGU ||  |     |                                                                                                           
                                            20-CGU||  |     |                                                                                                           
                                                 25-CGU     |                                                                                                           
                                                  26-CGU    |                                                                                                           
                                                     29-CGU |                                                                                                           
                                                           35-CGU                                                                                                       


Chain T from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeee.....eeeeeeeee.....eeeeeee...eeehhhhhh......eeeeeeeee......eeee....hhhhhh......eeeeeee..eeeeee...eeeeee..eeeehhhhhhhhheeeeeeee......eeeee...eeeee......eeeeeeee...............ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ibl T    6 TVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPAGNGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVECM  210
                                    15        25        35        45        55        65        75      ||92       102       112       122       132       142       152       162       172       182       192       202        
                                                                                                       82|                                                                                                                        
                                                                                                        90
   Legend:   → Mismatch (orange background)
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    → 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 4IBL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (61, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA7_HUMAN | P08709: 1bf9 1cvw 1dan 1dva 1f7e 1f7m 1fak 1ff7 1ffm 1j9c 1jbu 1kli 1klj 1nl8 1o5d 1qfk 1w0y 1w2k 1w7x 1w8b 1wqv 1wss 1wtg 1wun 1wv7 1ygc 1z6j 2a2q 2aei 2aer 2b7d 2b8o 2bz6 2c4f 2ec9 2f9b 2fir 2flb 2flr 2puq 2zp0 2zwl 2zzu 3ela 3th2 3th3 3th4 4ish 4isi 4jyu 4jyv 4jzd 4jze 4jzf 4na9 4ng9 4nga 4x8s 4x8t 4x8u 4x8v 4ylq 4yt6 4yt7 4z6a 4zma 4zxx 4zxy 5i46 5l2y 5l2z 5l30 5pa8 5pa9 5paa 5pab 5pac 5pae 5paf 5pag 5pai 5paj 5pak 5pam 5pan 5pao 5paq 5par 5pas 5pat 5pau 5pav 5paw 5pax 5pay 5pb0 5pb1 5pb2 5pb3 5pb4 5pb5 5pb6 5tqe 5tqf 5tqg 5u6j
        TF_HUMAN | P13726: 1ahw 1boy 1dan 1fak 1j9c 1jps 1nl8 1o5d 1tfh 1uj3 1w0y 1w2k 1wqv 1wss 1wtg 1wun 1wv7 1z6j 2a2q 2aei 2aer 2b7d 2b8o 2c4f 2cef 2ceh 2cez 2cfj 2ec9 2f9b 2fir 2flb 2flr 2hft 2puq 2zp0 2zwl 2zzu 3ela 3th2 3th3 3th4 4m7l 4ylq 4z6a 4zma 5w06

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4IBL)