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(-) Description

Title :  DETECTING ALLOSTERIC SITES OF HIV-1 REVERSE TRANSCRIPTASE BY X-RAY CRYSTALLOGRAPHIC FRAGMENT SCREENING
 
Authors :  J. D. Bauman, D. Patel, M. Fromer, E. Arnold
Date :  15 Dec 12  (Deposition) - 06 Feb 13  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna-Directed Dna Polymerase, Dna Polymerase, Endonuclease, Hydrolase, Multifunctional Enzyme, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Bauman, D. Patel, C. Dharia, M. W. Fromer, S. Ahmed, Y. Frenkel, R. S. Vijayan, J. T. Eck, W. C. Ho, K. Das, A. J. Shatkin, E. Arnold
Detecting Allosteric Sites Of Hiv-1 Reverse Transcriptase B X-Ray Crystallographic Fragment Screening.
J. Med. Chem. V. 56 2738 2013
PubMed-ID: 23342998  |  Reference-DOI: 10.1021/JM301271J

(-) Compounds

Molecule 1 - EXORIBONUCLEASE H, P66 RT
    Chains: A
    EC Number: 2.7.7.49, 2.7.7.7, 3.1.26.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDF-2
    Expression System Strain: BL21(RIL)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: P66 (UNP RESIDUES 600-1154)
    Gene: GAG-POL, POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11678
    Strain: BH10
    Synonym: REVERSE TRANSCRIPTASE/RIBONUCLEASE H
 
Molecule 2 - GAG-POL POLYPROTEIN
    Chains: B
    EC Number: 2.7.7.49, 2.7.7.7, 3.1.26.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDF-2
    Expression System Strain: BL21(RIL)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: P51 (UNP RESIDUES 600-1027)
    Gene: GAG-POL, POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11678
    Strain: BH10
    Synonym: PR160GAG-POL, MATRIX PROTEIN P17, MA, CAPSID PROTEIN P24, CA, SPACER PEPTIDE P2, NUCLEOCAPSID PROTEIN P7, NC, TRANSFRAME PEPTIDE, TF, P6-POL, P6*, PROTEASE, PR, RETROPEPSIN, REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEASE H, P66 RT, P51 RT, P15, INTEGRASE, IN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1DMS11Ligand/IonDIMETHYL SULFOXIDE
2FMQ2Ligand/Ion[1-(4-FLUOROPHENYL)-5-METHYL-1H-PYRAZOL-4-YL]METHANOL
3MG1Ligand/IonMAGNESIUM ION
4T271Ligand/Ion4-{[4-({4-[(E)-2-CYANOETHENYL]-2,6-DIMETHYLPHENYL}AMINO)PYRIMIDIN-2-YL]AMINO}BENZONITRILE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:100 , LYS A:101 , LYS A:103 , TYR A:181 , TYR A:188 , PHE A:227 , TRP A:229 , LEU A:234 , HIS A:235 , PRO A:236 , TYR A:318 , HOH A:925 , GLU B:138 , HOH B:632BINDING SITE FOR RESIDUE T27 A 601
02AC2SOFTWARELEU A:469 , GLN A:480 , LEU A:484 , GLU A:516 , LEU A:517 , GLN A:520BINDING SITE FOR RESIDUE FMQ A 602
03AC3SOFTWARETRP A:401 , LEU A:425 , TRP A:426 , TYR A:427 , GLN A:509 , ASP A:511BINDING SITE FOR RESIDUE DMS A 603
04AC4SOFTWAREGLN A:428 , LEU A:525 , LYS A:528 , GLU A:529BINDING SITE FOR RESIDUE DMS A 604
05AC5SOFTWARELYS A:331 , GLY A:333 , GLN A:334BINDING SITE FOR RESIDUE DMS A 605
06AC6SOFTWARETHR A:473 , ASN A:474 , GLN A:475 , HOH A:1012BINDING SITE FOR RESIDUE DMS A 606
07AC7SOFTWAREASP A:443 , ASP A:498 , ASP A:549 , HOH A:866 , HOH A:967 , HOH A:1031BINDING SITE FOR RESIDUE MG A 607
08AC8SOFTWARETHR A:377 , ILE A:380 , TRP B:24 , PRO B:25 , GLU B:399 , THR B:400 , TRP B:402 , DMS B:502 , HOH B:628BINDING SITE FOR RESIDUE FMQ B 501
09AC9SOFTWARETHR B:27 , THR B:400 , TRP B:401 , GLU B:404 , FMQ B:501BINDING SITE FOR RESIDUE DMS B 502
10BC1SOFTWAREGLN A:85 , TYR B:56 , LYS B:126BINDING SITE FOR RESIDUE DMS B 503
11BC2SOFTWAREILE A:380 , VAL A:381 , PRO B:25 , LEU B:26 , PRO B:133 , SER B:134 , ILE B:135 , HOH B:810BINDING SITE FOR RESIDUE DMS B 504
12BC3SOFTWARELEU B:234 , HIS B:235 , TRP B:239BINDING SITE FOR RESIDUE DMS B 505
13BC4SOFTWAREGLU A:138 , GLN B:269 , LEU B:422 , TRP B:426BINDING SITE FOR RESIDUE DMS B 506
14BC5SOFTWAREPRO B:243 , ILE B:244 , VAL B:245 , LYS B:263 , TRP B:426 , TYR B:427 , GLN B:428BINDING SITE FOR RESIDUE DMS B 507
15BC6SOFTWAREGLN B:242 , TYR B:271 , ASN B:348 , HOH B:642BINDING SITE FOR RESIDUE DMS B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IFV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:225 -Pro A:226
2Pro A:420 -Pro A:421

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IFV)

(-) 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:556
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4ifva1 A:-1-429 automated matches                                                                                                                                                                                                                                                                                                                                                                                                             d4ifva2 A:430-554 automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................hhhhhhhhhhhhhhhhhh..eee..........eeeee......eeeee.hhhhhhhh...........hhhhh....eeeeeehhhhhh.......hhhhhheee.hhhhh...eeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh...............eee..eee....eee...........hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhhhhhhhhhh...............eeeeeeee..eeeeeee.....eeeeeeee.....eehhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh........eee......................eeeeeeee......eeeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh...ee.hhhhhhhhhhhhhh.eeeeee........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ifv A  -1 MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA 554
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548      


Chain B from PDB  Type:PROTEIN  Length:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4ifvb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhhhhh..eee..........eeeee......eeeee.hhhhhhhh..............hhhhh.eeeeee.hhhhhhh.....hhhhhheee.hhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee..hhhhhhhhhhhhhhhhhhh.......eeehhhhh............eehhhhhhhhhhhhhhhhhh....hhhhhhhhh.......ee..hhhhhhhhhhhhhhh...............eeeeeeee..eeeeeeeee..eeeeeeee........hhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh......eeee......hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ifv B   5 IETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQ 428
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214|      236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426  
                                                                                                                                                                                                                                           214|                                                                                                                                                                                                         
                                                                                                                                                                                                                                            227
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

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
        POL_HV1B1 | P03366: 1a9m 1ajv 1ajx 1axa 1bqm 1bqn 1d4h 1d4i 1d4j 1dlo 1dw6 1ebk 1ebw 1eby 1ebz 1ec0 1ec1 1ec2 1ec3 1eet 1g35 1gnm 1gnn 1gno 1har 1hbv 1hef 1heg 1hih 1hmv 1hni 1hnv 1hos 1hps 1hpz 1hqe 1hqu 1hrh 1hte 1htf 1htg 1hvi 1hvk 1hvp 1hvu 1hys 1ikv 1ikw 1ikx 1iky 1j5o 1kjh 1mer 1mes 1met 1meu 1n5y 1n6q 1npa 1npv 1npw 1qe1 1qmc 1r0a 1rdh 1rtd 1rvl 1rvm 1rvn 1rvo 1rvp 1rvq 1rvr 1s6p 1s6q 1s9e 1s9g 1sbg 1suq 1sv5 1t03 1t05 1t7k 1tv6 1tvr 1uwb 1w5v 1w5w 1w5x 1w5y 1yt9 1zp8 1zpa 1zsf 1zsr 2aqu 2b5j 2b6a 2ban 2bbb 2be2 2exf 2fde 2g69 2hb3 2hmi 2hnz 2hs1 2hs2 2i4d 2i4u 2i4v 2i4w 2i4x 2i5j 2iaj 2ic3 2idw 2ien 2ieo 2jzw 2l45 2l46 2l4l 2uxz 2uy0 2vg5 2vg6 2vg7 2wkz 2wl0 2x4u 2xye 2xyf 2ykm 2ykn 2zd1 2ze2 3avi 3bgr 3dlk 3gga 3ggv 3ggx 3hvt 3ig1 3irx 3is9 3isn 3ith 3jsm 3jyt 3k2p 3k4v 3kle 3klf 3klg 3klh 3kli 3ndt 3nu3 3nu4 3nu5 3nu6 3nu9 3nuj 3nuo 3ok9 3psu 3qaa 3qlh 3qo9 3tkg 3tkw 3tl9 3tlh 3v4i 3v6d 3v81 3zps 3zpt 3zpu 4coe 4cp7 4cpq 4cpr 4cps 4cpt 4cpu 4cpw 4cpx 4dg1 4g1q 4g8g 4g8i 4g9d 4g9f 4h4m 4h4o 4i2p 4i2q 4icl 4id5 4idk 4ify 4ig0 4ig3 4kfb 4kko 4ko0 4lsl 4lsn 4mfb 4o44 4o4g 4ojr 4pqu 4puo 4pwd 4q0b 4qag 4r5p 4rw4 4rw6 4rw7 4rw8 4rw9 4u8w 4we1 4ye3 4yhq 4zip 4zls 5agz 5ah6 5ah7 5ah8 5ah9 5aha 5ahb 5ahc 5bry 5bs4 5c24 5c25 5c42 5cym 5cyq 5d3g 5fdl 5hbm 5hlf 5hp1 5hro 5i3u 5i42 5j1e 5jfp 5jfu 5jg1 5t6z 5t70 5tep 5ter 5tuq 5tw3 5txl 5txm 5txn 5txo 5txp

(-) Related Entries Specified in the PDB File

4icl 4id5 4idk 4ify 4ig0 4ig3 4ig7