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(-) Description

Title :  PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA IN CLOSED CONFORMATION WITH GAPPED DNA SUBSTRATE INCOMING (-)3TC-TP AND MN2+.
 
Authors :  R. Vyas, Z. Suo
Date :  11 Sep 16  (Deposition) - 11 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,D,P,T
Keywords :  X-Family, Pol Beta, Dna Polymerase Beta, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Reed, R. Vyas, A. T. Raper, Z. Suo
Structural Insights Into The Post-Chemistry Steps Of Nucleotide Incorporation Catalyzed By A Dna Polymerase.
J. Am. Chem. Soc. V. 139 465 2017
PubMed-ID: 27959534  |  Reference-DOI: 10.1021/JACS.6B11258

(-) Compounds

Molecule 1 - DNA POLYMERASE BETA
    Chains: A
    EC Number: 2.7.7.7, 4.2.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: POLB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 5-MER PHOSPHORYLATED DOWNSTREAM PRIME
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC DNA
    Synthetic: YES
 
Molecule 3 - 10- MER PRIMER
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC DNA
    Synthetic: YES
 
Molecule 4 - 16- MER TEMPLATE
    Chains: T
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
11RZ1Ligand/Ion[[(2R,5S)-5-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-1,3-OXATHIOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]PHOSPHONO HYDROGEN PHOSPHATE
2ACT6Ligand/IonACETATE ION
3CL2Ligand/IonCHLORIDE ION
4MN6Ligand/IonMANGANESE (II) ION
5NA5Ligand/IonSODIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:179 , SER A:180 , ARG A:183 , SER A:188 , GLY A:189 , ASP A:190 , ASP A:192 , TYR A:271 , PHE A:272 , ASP A:276 , ASN A:279 , MN A:405 , MN A:406 , HOH A:513 , HOH A:514 , HOH A:530 , HOH A:537 , HOH A:557 , HOH A:600 , DC P:10 , DG T:6binding site for residue 1RZ A 401
02AC2SOFTWAREHIS A:337 , HIS A:339 , HOH A:511 , HOH A:647binding site for residue MN A 402
03AC3SOFTWAREGLU A:117 , ASP A:321 , ACT A:417 , HOH A:535 , HOH A:624binding site for residue MN A 403
04AC4SOFTWARELYS A:48 , HIS A:336 , HIS A:338 , HOH A:592binding site for residue MN A 404
05AC5SOFTWAREASP A:190 , ASP A:192 , 1RZ A:401 , MN A:406 , HOH A:530binding site for residue MN A 405
06AC6SOFTWAREASP A:190 , ASP A:192 , ASP A:256 , 1RZ A:401 , MN A:405 , HOH A:557 , HOH A:603 , DC P:10binding site for residue MN A 406
07AC7SOFTWAREHIS A:285 , GLU A:288binding site for residue MN A 407
08AC8SOFTWAREASP A:130 , ASP A:314 , HOH A:520 , HOH A:564 , HOH A:644binding site for residue NA A 408
09AC9SOFTWAREASP A:145 , HIS A:252 , HOH A:590binding site for residue NA A 409
10AD1SOFTWARELYS A:60 , LEU A:62 , VAL A:65 , DC D:3 , HOH D:112binding site for residue NA A 410
11AD2SOFTWARETHR A:101 , VAL A:103 , ILE A:106 , HOH A:650 , DG P:9 , HOH P:106binding site for residue NA A 411
12AD3SOFTWAREASP A:91 , GLN A:157 , ACT A:416 , HOH A:542 , HOH A:550 , HOH A:613binding site for residue NA A 412
13AD4SOFTWAREASN A:294 , THR A:297binding site for residue CL A 413
14AD5SOFTWAREALA A:32 , ILE A:33 , HIS A:34binding site for residue CL A 414
15AD6SOFTWAREHIS A:34 , ASN A:37 , ALA A:38 , LYS A:41 , LYS A:280 , HOH A:538 , DG D:1 , DC T:5binding site for residue ACT A 415
16AD7SOFTWAREVAL A:29 , ASP A:91 , GLN A:157 , ASP A:160 , NA A:412 , HOH A:550binding site for residue ACT A 416
17AD8SOFTWAREGLU A:117 , ASP A:321 , TYR A:322 , MN A:403binding site for residue ACT A 417
18AD9SOFTWARETYR A:36 , HOH A:504binding site for residue ACT A 418
19AE1SOFTWARELYS A:127 , HOH A:505binding site for residue ACT A 419
20AE2SOFTWAREASP A:246 , TRP A:325 , LYS A:326 , ARG A:328 , HOH A:570 , HOH A:653binding site for residue ACT A 420

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TB8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:208 -Lys A:209
2Gly A:274 -Ser A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TB8)

(-) Exons   (0, 0)

(no "Exon" information available for 5TB8)

(-) 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee..eeeeee.........hhhhhhhhhhhhh..eeeeeee...eeeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee..............hhhhhhhhh.....hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tb8 A   9 ETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH 341
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198     ||211       221       231       241    || 253       263       273       283       293       303       313       323       333        
                                                                                                                                                                                                                             204|                                   246|                                                                                            
                                                                                                                                                                                                                              208                                    249                                                                                            


Chain D from PDB  Type:DNA  Length:5
                                     
                 5tb8 D   1 GTCGG   5


Chain P from PDB  Type:DNA  Length:10
                                          
                 5tb8 P   1 GCTGATGCGC  10
                                    10


Chain T from PDB  Type:DNA  Length:16
                                                
                 5tb8 T   1 CCGACGGCGCATCAGC  16
                                    10
   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 5TB8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TB8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TB8)

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)

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

UniProtKB/Swiss-Prot
        DPOLB_HUMAN | P06746: 1bpx 1bpy 1bpz 1mq2 1mq3 1tv9 1tva 1zjm 1zjn 1zqa 1zqb 1zqc 1zqd 1zqe 1zqf 1zqg 1zqh 1zqi 1zqj 1zqk 1zql 1zqm 1zqn 1zqo 1zqp 1zqq 1zqr 1zqs 1zqt 2fmp 2fmq 2fms 2i9g 2iso 2isp 2p66 2pxi 3c2k 3c2l 3c2m 3gdx 3isb 3isc 3isd 3jpn 3jpo 3jpp 3jpq 3jpr 3jps 3jpt 3lk9 3mby 3ogu 3rh4 3rh5 3rh6 3rje 3rjf 3rjg 3rjh 3rji 3rjj 3rjk 3tfr 3tfs 4do9 4doa 4dob 4doc 4f5n 4f5o 4f5p 4f5q 4f5r 4gxi 4gxj 4gxk 4jwm 4jwn 4kld 4kle 4klf 4klg 4klh 4kli 4klj 4kll 4klm 4klo 4klq 4kls 4klt 4klu 4lvs 4m2y 4m47 4m9g 4m9h 4m9j 4m9l 4m9n 4mf2 4mf8 4mfa 4mfc 4mff 4nlk 4nln 4nlz 4nm1 4nm2 4nxz 4ny8 4o5c 4o5e 4o5k 4o9m 4p2h 4pgq 4pgx 4pgy 4ph5 4pha 4phd 4phe 4php 4ppx 4r63 4r64 4r65 4r66 4rpx 4rpy 4rpz 4rq0 4rq1 4rq2 4rq3 4rq4 4rq5 4rq6 4rq7 4rq8 4rt2 4rt3 4tup 4tuq 4tur 4tus 4uaw 4uay 4uaz 4ub1 4ub2 4ub3 4ub4 4ub5 4ubb 4ubc 4ymm 4ymn 4ymo 4yn4 4z6c 4z6d 4z6e 4z6f 5bol 5bom 5bpc 5db6 5db7 5db8 5db9 5dba 5dbb 5dbc 5eoz 5hhh 5hhi 5j0o 5j0p 5j0q 5j0r 5j0s 5j0t 5j0u 5j0w 5j0x 5j0y 5j29 5j2a 5j2b 5j2c 5j2d 5j2e 5j2f 5j2g 5j2h 5j2i 5j2j 5j2k 5tb9 5tba 5tbb 5tbc 5tzv 5u2r 5u2s 5u2t 5u8g 5u8h 5u8i 5u9h 5v1f 5v1g 5v1h 5v1i 5v1j 5v1n 5v1o 5v1p 5v1r 5vez 7ice 7icf 7icg 7ich 7ici 7icj 7ick 7icl 7icm 7icn 7ico 7icp 7icq 7icr 7ics 7ict 7icu 7icv 8ica 8icb 8icc 8ice 8icf 8icg 8ich 8ici 8icj 8ick 8icl 8icm 8icn 8ico 8icp 8icq 8icr 8ics 8ict 8icu 8icv 8icw 8icx 8icy 8icz 9ica 9icb 9icc 9ice 9icf 9icg 9ich 9ici 9icj 9ick 9icl 9icm 9icn 9ico 9icp 9icq 9icr 9ics 9ict 9icu 9icv 9icw 9icx 9icy

(-) Related Entries Specified in the PDB File

5tb9 5tba 5tbb 5tbc