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(-) Description

Title :  X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN THROMBIN AND THE TBA DELETION MUTANT LACKING THYMINE 3 NUCLEOBASE
 
Authors :  A. Pica, I. Russo Krauss, A. Merlino, F. Sica
Date :  31 Jul 13  (Deposition) - 08 Jan 14  (Release) - 08 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Protein-Dna Complex, Dna Aptamer, G-Quadruplex, Tba Deletion Mutant, Serine Protease, Hydrolase, Blood Coagulation, Blood, Hydrolase-Dna Complex, Hydrolase-Hydrolase Inhibitor-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pica, I. Russo Krauss, A. Merlino, S. Nagatoishi, N. Sugimoto, F. Sica
Dissecting The Contribution Of Thrombin Exosite I In The Recognition Of Thrombin Binding Aptamer.
Febs J. V. 280 6581 2013
PubMed-ID: 24128303  |  Reference-DOI: 10.1111/FEBS.12561

(-) Compounds

Molecule 1 - THROMBIN LIGHT CHAIN
    Chains: A, C
    EC Number: 3.4.21.5
    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
 
Molecule 2 - THROMBIN HEAVY CHAIN
    Chains: B, D
    EC Number: 3.4.21.5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN HEAVY CHAIN
 
Molecule 3 - THROMBIN BINDING APTAMER (TBA)
    Chains: E, F
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
10G62Ligand/IonD-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
23DR2Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3K2Ligand/IonPOTASSIUM ION
4NA2Ligand/IonSODIUM ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
10G61Ligand/IonD-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
23DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3K-1Ligand/IonPOTASSIUM ION
4NA-1Ligand/IonSODIUM ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
10G61Ligand/IonD-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
23DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3K-1Ligand/IonPOTASSIUM ION
4NA-1Ligand/IonSODIUM ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:60GBINDING SITE FOR RESIDUE NAG B 301
2AC2SOFTWAREHIS B:57 , TYR B:60A , TRP B:60D , GLU B:97A , LEU B:99 , ASP B:189 , ALA B:190 , GLY B:193 , SER B:195 , SER B:214 , TRP B:215 , GLY B:216 , GLY B:219 , GLY B:226 , HOH B:408 , HOH B:409 , HOH B:410BINDING SITE FOR RESIDUE 0G6 B 302
3AC3SOFTWAREARG B:221 , LYS B:224 , HOH B:443 , HOH B:446 , HOH B:452 , HOH B:482BINDING SITE FOR RESIDUE NA B 303
4AC4SOFTWAREASN D:60GBINDING SITE FOR RESIDUE NAG D 301
5AC5SOFTWAREHIS D:57 , TYR D:60A , TRP D:60D , GLU D:97A , LEU D:99 , ASP D:189 , ALA D:190 , GLY D:193 , SER D:195 , SER D:214 , TRP D:215 , GLY D:216 , GLY D:219 , GLY D:226 , HOH D:414 , HOH D:415 , HOH D:416BINDING SITE FOR RESIDUE 0G6 D 302
6AC6SOFTWAREARG D:221 , LYS D:224 , HOH D:459 , HOH D:460 , HOH D:461BINDING SITE FOR RESIDUE NA D 303
7AC7SOFTWAREDG E:1 , DG E:2 , DG E:5 , DG E:6 , DG E:10 , DG E:11 , DG E:14 , DG E:15BINDING SITE FOR RESIDUE K E 101
8AC8SOFTWAREDG F:1 , DG F:2 , DG F:5 , DG F:6 , DG F:10 , DG F:11 , DG F:14 , DG F:15BINDING SITE FOR RESIDUE K F 101

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:1 -B:122
2B:42 -B:58
3B:168 -B:182
4B:191 -B:220
5C:1 -D:122
6D:42 -D:58
7D:168 -D:182
8D:191 -D:220

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser B:36A-Pro B:37
2Ser D:36A-Pro D:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4LZ4)

(-) 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:34
                                                                   
               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
                4lz4 A   1H TFGSGEADCGLRPLFEKKSLEDKTERELLESYID  14L
                            |||||||| 2        12  |||||14H||||
                            ||||||||            14A||||||14J||
                           1H|||||||             14B||||||14K|
                            1G||||||              14C||||||14L
                             1F|||||               14D|||||   
                              1E||||                14E||||   
                               1D|||                 14F|||   
                                1C||                  14G||   
                                 1B|                   14H|   
                                  1A                    14I   


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeeee....eeeehhhhheehhhhee.hhh.eeeee.............eeeeeeeeee..............eeeee................hhhhhhhhh....eeeeee....................eeeeee..hhhhhhhhh.......eeee..hhhhh............eeeee......eeeeeeeee..........eeeee...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4lz4 B   16 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG  246
                                    25        35 |      44        54      |60D|||||   65        75  |     84        94   |   103       113       123      |130       140      149A||||   155       165       175      184A  |||| 190       200    || 208       219 |     228       238        
                                               36A                      60A||||||||               77A                  97A                             129A||                 149A||||                                184A  ||||               204A|          217| |                          
                                                                         60B|||||||                                                                     129B|                  149B|||                                   186A|||                204B           219 |                          
                                                                          60C||||||                                                                      129C                   149C||                                    186B||                                221A                          
                                                                           60D|||||                                                                                              149D|                                     186C|                                                              
                                                                            60E||||                                                                                               149E                                      186D                                                              
                                                                             60F|||                                                                                                                                                                                                           
                                                                              60G||                                                                                                                                                                                                           
                                                                               60H|                                                                                                                                                                                                           
                                                                                60I                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:34
                                                                   
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....hhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                4lz4 C   1H TFGSGEADCGLRPLFEKKSLEDKTERELLESYID  14L
                            |||||||| 2        12  |||||14H||||
                           1H|||||||            14A||||||14J||
                            1G||||||             14B||||||14K|
                             1F|||||              14C||||||14L
                              1E||||               14D|||||   
                               1D|||                14E||||   
                                1C||                 14F|||   
                                 1B|                  14G||   
                                  1A                   14H|   
                                                        14I   


Chain D from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeeee....eeeehhhhheehhhhee.hhh.eeeee.............eeeeeeeeee..............eeeee................hhhhhhhhh....eeeeee....................eeeeee..hhhhhhhh........eeee..hhhhh............eeeee......eeeeeeeee..........eeeeehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4lz4 D   16 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG  246
                                    25        35 |      44        54      |60D|||||   65        75  |     84        94   |   103       113       123      |130       140      149A||||   155       165       175      184A  |||| 190       200    || 208       219 |     228       238        
                                               36A                      60A||||||||               77A                  97A                             129A||                 149A||||                                184A  ||||               204A|          217| |                          
                                                                         60B|||||||                                                                     129B|                  149B|||                                   186A|||                204B           219 |                          
                                                                          60C||||||                                                                      129C                   149C||                                    186B||                                221A                          
                                                                           60D|||||                                                                                              149D|                                     186C|                                                              
                                                                            60E||||                                                                                               149E                                      186D                                                              
                                                                             60F|||                                                                                                                                                                                                           
                                                                              60G||                                                                                                                                                                                                           
                                                                               60H|                                                                                                                                                                                                           
                                                                                60I                                                                                                                                                                                                           


Chain E from PDB  Type:DNA  Length:15
                                                
                4lz4 E    1 GGxTGGTGTGGTTGG   15
                              |     10     
                              3-3DR        


Chain F from PDB  Type:DNA  Length:15
                                                
                4lz4 F    1 GGxTGGTGTGGTTGG   15
                              |     10     
                              3-3DR
   Legend:   → Mismatch (orange background)
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  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 4LZ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LZ4)

(-) Gene Ontology  (51, 51)

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  4lz4
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  THRB_HUMAN | P00734
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        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 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

3qlp 4dih 4dii 4lz1