0.015954 0.009211 0.000000 0.000000 0.018422 0.000000 0.000000 0.000000 0.011977 0.00000 0.00000 0.00000 Swairjo, M.A. Abdel-Meguid, S.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 62.680 62.680 83.490 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C31 H42 N4 O4 534.690 (2R,4S,5S,1'S)-2-PHENYLMETHYL-4-HYDROXY-5-(TERT-BUTOXYCARBONYL)AMINO-6-PHENYL HEXANOYL-N-(1'-IMIDAZO-2-YL)-2'-METHYLPROPANAMIDE non-polymer C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Biochemistry BICHAW 0033 0006-2960 37 10928 10936 10.1021/bi980784h 9692985 Structural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease. 1998 US Biochemistry BICHAW 0033 0006-2960 36 5128 Identification of a Loop Outside the Active Site Cavity of the Human Immunodeficiency Virus Proteases which Confers Inhibitor Specificity 1997 10.2210/pdb1bdr/pdb pdb_00001bdr 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 292 1 MIRRORS IMAGE PLATE 1997-07 MARRESEARCH NI FILTER M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RUH2R 10669.604 HIV-1 PROTEASE 3.4.23.16 T31S, L33V, E34T, E35G, M36I, S37E 2 man polymer 534.690 (2R,4S,5S,1'S)-2-PHENYLMETHYL-4-HYDROXY-5-(TERT-BUTOXYCARBONYL)AMINO-6-PHENYL HEXANOYL-N-(1'-IMIDAZO-2-YL)-2'-METHYLPROPANAMIDE 1 syn non-polymer 18.015 water 56 nat water no no PQITLWQRPLVTIKIGGQLKEALLDTGADDSVVAGIELPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF PQITLWQRPLVTIKIGGQLKEALLDTGADDSVVAGIELPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Lentivirus IIIB Escherichia sample HIV-1 PROTEASE 11676 Human immunodeficiency virus 1 562 Escherichia coli BMH 71-18 MUTS M13MP19PRO4 POTSKF33 1 2.22 45 VAPOR DIFFUSION, HANGING DROP 5.2 HANGING DROP VAPOUR DIFFUSION, BY MIXING EQUAL VOLUMES OF RESERVOIR AND SAMPLE, 21 DEG. C RESERVOIR: 28% 3.5 MG/ML PROTEIN/INHIBITOR COMPLEX AT 1:5 MOLAR RATIO., pH 5.2, vapor diffusion - hanging drop, temperature 294K 294 database_2 pdbx_database_status struct_ref_seq_dif struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Refinement description 1 0 1998-10-14 1 1 2008-03-24 1 2 2011-07-13 1 3 2021-11-03 1 4 2023-08-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1998-05-10 REL REL IM1 (2R,4S,5S,1'S)-2-PHENYLMETHYL-4-HYDROXY-5-(TERT-BUTOXYCARBONYL)AMINO-6-PHENYL HEXANOYL-N-(1'-IMIDAZO-2-YL)-2'-METHYLPROPANAMIDE HOH water 1SBG PDB ENTRY 1SBG PDB experimental model IM1 400 2 IM1 IM1 400 B HOH 500 3 HOH HOH 500 A HOH 501 3 HOH HOH 501 A HOH 503 3 HOH HOH 503 A HOH 504 3 HOH HOH 504 A HOH 507 3 HOH HOH 507 A HOH 508 3 HOH HOH 508 A HOH 509 3 HOH HOH 509 A HOH 510 3 HOH HOH 510 A HOH 511 3 HOH HOH 511 A HOH 512 3 HOH HOH 512 A HOH 513 3 HOH HOH 513 A HOH 518 3 HOH HOH 518 A HOH 519 3 HOH HOH 519 A HOH 521 3 HOH HOH 521 A HOH 526 3 HOH HOH 526 A HOH 527 3 HOH HOH 527 A HOH 528 3 HOH HOH 528 A HOH 529 3 HOH HOH 529 A HOH 530 3 HOH HOH 530 A HOH 531 3 HOH HOH 531 A HOH 532 3 HOH HOH 532 A HOH 533 3 HOH HOH 533 A HOH 534 3 HOH HOH 534 A HOH 536 3 HOH HOH 536 A HOH 537 3 HOH HOH 537 A HOH 538 3 HOH HOH 538 A HOH 539 3 HOH HOH 539 A HOH 542 3 HOH HOH 542 A HOH 543 3 HOH HOH 543 A HOH 546 3 HOH HOH 546 A HOH 547 3 HOH HOH 547 A HOH 550 3 HOH HOH 550 A HOH 552 3 HOH HOH 552 A HOH 553 3 HOH HOH 553 A HOH 555 3 HOH HOH 555 A HOH 502 3 HOH HOH 502 B HOH 505 3 HOH HOH 505 B HOH 506 3 HOH HOH 506 B HOH 514 3 HOH HOH 514 B HOH 515 3 HOH HOH 515 B HOH 516 3 HOH HOH 516 B HOH 520 3 HOH HOH 520 B HOH 522 3 HOH HOH 522 B HOH 523 3 HOH HOH 523 B HOH 524 3 HOH HOH 524 B HOH 525 3 HOH HOH 525 B HOH 535 3 HOH HOH 535 B HOH 540 3 HOH HOH 540 B HOH 541 3 HOH HOH 541 B HOH 544 3 HOH HOH 544 B HOH 545 3 HOH HOH 545 B HOH 548 3 HOH HOH 548 B HOH 549 3 HOH HOH 549 B HOH 551 3 HOH HOH 551 B HOH 554 3 HOH HOH 554 B HOH 556 3 HOH HOH 556 B PRO 1 n 1 PRO 1 A GLN 2 n 2 GLN 2 A ILE 3 n 3 ILE 3 A THR 4 n 4 THR 4 A LEU 5 n 5 LEU 5 A TRP 6 n 6 TRP 6 A GLN 7 n 7 GLN 7 A ARG 8 n 8 ARG 8 A PRO 9 n 9 PRO 9 A LEU 10 n 10 LEU 10 A VAL 11 n 11 VAL 11 A THR 12 n 12 THR 12 A ILE 13 n 13 ILE 13 A LYS 14 n 14 LYS 14 A ILE 15 n 15 ILE 15 A GLY 16 n 16 GLY 16 A GLY 17 n 17 GLY 17 A GLN 18 n 18 GLN 18 A LEU 19 n 19 LEU 19 A LYS 20 n 20 LYS 20 A GLU 21 n 21 GLU 21 A ALA 22 n 22 ALA 22 A LEU 23 n 23 LEU 23 A LEU 24 n 24 LEU 24 A ASP 25 n 25 ASP 25 A THR 26 n 26 THR 26 A GLY 27 n 27 GLY 27 A ALA 28 n 28 ALA 28 A ASP 29 n 29 ASP 29 A ASP 30 n 30 ASP 30 A SER 31 n 31 SER 31 A VAL 32 n 32 VAL 32 A VAL 33 n 33 VAL 33 A ALA 34 n 34 ALA 34 A GLY 35 n 35 GLY 35 A ILE 36 n 36 ILE 36 A GLU 37 n 37 GLU 37 A LEU 38 n 38 LEU 38 A PRO 39 n 39 PRO 39 A GLY 40 n 40 GLY 40 A ARG 41 n 41 ARG 41 A TRP 42 n 42 TRP 42 A LYS 43 n 43 LYS 43 A PRO 44 n 44 PRO 44 A LYS 45 n 45 LYS 45 A MET 46 n 46 MET 46 A ILE 47 n 47 ILE 47 A GLY 48 n 48 GLY 48 A GLY 49 n 49 GLY 49 A ILE 50 n 50 ILE 50 A GLY 51 n 51 GLY 51 A GLY 52 n 52 GLY 52 A PHE 53 n 53 PHE 53 A ILE 54 n 54 ILE 54 A LYS 55 n 55 LYS 55 A VAL 56 n 56 VAL 56 A ARG 57 n 57 ARG 57 A GLN 58 n 58 GLN 58 A TYR 59 n 59 TYR 59 A ASP 60 n 60 ASP 60 A GLN 61 n 61 GLN 61 A ILE 62 n 62 ILE 62 A LEU 63 n 63 LEU 63 A ILE 64 n 64 ILE 64 A GLU 65 n 65 GLU 65 A ILE 66 n 66 ILE 66 A CYS 67 n 67 CYS 67 A GLY 68 n 68 GLY 68 A HIS 69 n 69 HIS 69 A LYS 70 n 70 LYS 70 A ALA 71 n 71 ALA 71 A ILE 72 n 72 ILE 72 A GLY 73 n 73 GLY 73 A THR 74 n 74 THR 74 A VAL 75 n 75 VAL 75 A LEU 76 n 76 LEU 76 A VAL 77 n 77 VAL 77 A GLY 78 n 78 GLY 78 A PRO 79 n 79 PRO 79 A THR 80 n 80 THR 80 A PRO 81 n 81 PRO 81 A VAL 82 n 82 VAL 82 A ASN 83 n 83 ASN 83 A ILE 84 n 84 ILE 84 A ILE 85 n 85 ILE 85 A GLY 86 n 86 GLY 86 A ARG 87 n 87 ARG 87 A ASN 88 n 88 ASN 88 A LEU 89 n 89 LEU 89 A LEU 90 n 90 LEU 90 A THR 91 n 91 THR 91 A GLN 92 n 92 GLN 92 A ILE 93 n 93 ILE 93 A GLY 94 n 94 GLY 94 A CYS 95 n 95 CYS 95 A THR 96 n 96 THR 96 A LEU 97 n 97 LEU 97 A ASN 98 n 98 ASN 98 A PHE 99 n 99 PHE 99 A PRO 1 n 1 PRO 1 B GLN 2 n 2 GLN 2 B ILE 3 n 3 ILE 3 B THR 4 n 4 THR 4 B LEU 5 n 5 LEU 5 B TRP 6 n 6 TRP 6 B GLN 7 n 7 GLN 7 B ARG 8 n 8 ARG 8 B PRO 9 n 9 PRO 9 B LEU 10 n 10 LEU 10 B VAL 11 n 11 VAL 11 B THR 12 n 12 THR 12 B ILE 13 n 13 ILE 13 B LYS 14 n 14 LYS 14 B ILE 15 n 15 ILE 15 B GLY 16 n 16 GLY 16 B GLY 17 n 17 GLY 17 B GLN 18 n 18 GLN 18 B LEU 19 n 19 LEU 19 B LYS 20 n 20 LYS 20 B GLU 21 n 21 GLU 21 B ALA 22 n 22 ALA 22 B LEU 23 n 23 LEU 23 B LEU 24 n 24 LEU 24 B ASP 25 n 25 ASP 25 B THR 26 n 26 THR 26 B GLY 27 n 27 GLY 27 B ALA 28 n 28 ALA 28 B ASP 29 n 29 ASP 29 B ASP 30 n 30 ASP 30 B SER 31 n 31 SER 31 B VAL 32 n 32 VAL 32 B VAL 33 n 33 VAL 33 B ALA 34 n 34 ALA 34 B GLY 35 n 35 GLY 35 B ILE 36 n 36 ILE 36 B GLU 37 n 37 GLU 37 B LEU 38 n 38 LEU 38 B PRO 39 n 39 PRO 39 B GLY 40 n 40 GLY 40 B ARG 41 n 41 ARG 41 B TRP 42 n 42 TRP 42 B LYS 43 n 43 LYS 43 B PRO 44 n 44 PRO 44 B LYS 45 n 45 LYS 45 B MET 46 n 46 MET 46 B ILE 47 n 47 ILE 47 B GLY 48 n 48 GLY 48 B GLY 49 n 49 GLY 49 B ILE 50 n 50 ILE 50 B GLY 51 n 51 GLY 51 B GLY 52 n 52 GLY 52 B PHE 53 n 53 PHE 53 B ILE 54 n 54 ILE 54 B LYS 55 n 55 LYS 55 B VAL 56 n 56 VAL 56 B ARG 57 n 57 ARG 57 B GLN 58 n 58 GLN 58 B TYR 59 n 59 TYR 59 B ASP 60 n 60 ASP 60 B GLN 61 n 61 GLN 61 B ILE 62 n 62 ILE 62 B LEU 63 n 63 LEU 63 B ILE 64 n 64 ILE 64 B GLU 65 n 65 GLU 65 B ILE 66 n 66 ILE 66 B CYS 67 n 67 CYS 67 B GLY 68 n 68 GLY 68 B HIS 69 n 69 HIS 69 B LYS 70 n 70 LYS 70 B ALA 71 n 71 ALA 71 B ILE 72 n 72 ILE 72 B GLY 73 n 73 GLY 73 B THR 74 n 74 THR 74 B VAL 75 n 75 VAL 75 B LEU 76 n 76 LEU 76 B VAL 77 n 77 VAL 77 B GLY 78 n 78 GLY 78 B PRO 79 n 79 PRO 79 B THR 80 n 80 THR 80 B PRO 81 n 81 PRO 81 B VAL 82 n 82 VAL 82 B ASN 83 n 83 ASN 83 B ILE 84 n 84 ILE 84 B ILE 85 n 85 ILE 85 B GLY 86 n 86 GLY 86 B ARG 87 n 87 ARG 87 B ASN 88 n 88 ASN 88 B LEU 89 n 89 LEU 89 B LEU 90 n 90 LEU 90 B THR 91 n 91 THR 91 B GLN 92 n 92 GLN 92 B ILE 93 n 93 ILE 93 B GLY 94 n 94 GLY 94 B CYS 95 n 95 CYS 95 B THR 96 n 96 THR 96 B LEU 97 n 97 LEU 97 B ASN 98 n 98 ASN 98 B PHE 99 n 99 PHE 99 B author_and_software_defined_assembly PISA 2 dimeric 4960 -28 9240 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O ILE 3 A O ILE 3 B N LEU 97 B N LEU 97 B O THR 96 B O THR 96 A N ASN 98 A N ASN 98 A O VAL 11 A O VAL 11 A N ALA 22 A N ALA 22 1 A PRO 79 -69.38 81.44 1 B PRO 79 -56.22 31.00 PARHCSDX.PRO TOPHCSDX.PRO PARAM19.SOL TOPH19.SOL IM1.PARAM IM1.TOPOL PARAM19X.PRO TOPH19X.PRO 17.5 17.5 17.5 17.5 17.5 17.5 17.5 0.2550000 0.02 0.2010000 0.2010000 2.8 20.0 412 4054 10.0 95.6 RANDOM 0.0 1 RESTRAINED THROUGHOUT 0.0 DIFFERENCE FOURIER PDB ENTRY 1SBG 0.25 2.8 20.0 4 1584 78 0 1502 0.019 3.4 29.2 1.8 2.93 400 8 74.0 2.5 20.0 1BDR 6058 1.0 0.1200000 0.1200000 1 9.0 7.4 99.8 0.5300000 2.5 2.57 5.1 0.5300000 7.3 67.1 model building X-PLOR 3.1 refinement X-PLOR 3.1 data reduction DENZO data scaling SCALEPACK phasing X-PLOR 3.1 HIV-1 (2: 31, 33-37) PROTEASE COMPLEXED WITH INHIBITOR SB203386 1 N N 1 N N 2 N N 3 N N 3 N N A ARG 87 A ARG 87 HELX_P A ILE 93 A ILE 93 1 1 7 B ARG 87 B ARG 87 HELX_P B LEU 90 B LEU 90 1 2 4 HYDROLASE HYDROLASE, AIDS, POLYPROTEIN, ASPARTYL PROTEASE, ACID PROTEASE, HYDROXYETHYLENE ISOSTERE INHIBITOR, SUBSTRATE ANALOGUE INHIBITOR POL_HV1B5 UNP 1 1 P04587 FFREDLAFLQGKAREFSSEQTRANSPTISSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQITLWQRPLVT IKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQ IGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRK LVDFRELNRRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGSGYQYNVLPQGW KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYE LHPDKWTIQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEP VHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPI QKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAASRETKLGKAGYVTNRGRQKVVTLTHTT NQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS AGIRKILFLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVI LVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSATVKAACWWAGIKQEFGIPYNPQSQGVVES MNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNP LWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED 69 167 1BDR 1 99 P04587 A 1 1 99 69 167 1BDR 1 99 P04587 B 1 1 99 1 THR engineered mutation SER 31 1BDR A P04587 UNP 99 31 1 LEU engineered mutation VAL 33 1BDR A P04587 UNP 101 33 1 GLU conflict ALA 34 1BDR A P04587 UNP 102 34 1 GLU engineered mutation GLY 35 1BDR A P04587 UNP 103 35 1 MET engineered mutation ILE 36 1BDR A P04587 UNP 104 36 1 SER engineered mutation GLU 37 1BDR A P04587 UNP 105 37 2 THR engineered mutation SER 31 1BDR B P04587 UNP 99 31 2 LEU engineered mutation VAL 33 1BDR B P04587 UNP 101 33 2 GLU conflict ALA 34 1BDR B P04587 UNP 102 34 2 GLU engineered mutation GLY 35 1BDR B P04587 UNP 103 35 2 MET engineered mutation ILE 36 1BDR B P04587 UNP 104 36 2 SER engineered mutation GLU 37 1BDR B P04587 UNP 105 37 3 2 anti-parallel anti-parallel anti-parallel A GLN 2 A GLN 2 A THR 4 A THR 4 B THR 96 B THR 96 B ASN 98 B ASN 98 A THR 96 A THR 96 A ASN 98 A ASN 98 A LEU 10 A LEU 10 A ILE 15 A ILE 15 A GLN 18 A GLN 18 A LEU 23 A LEU 23 IM1 BINDING SITE. Unknown 2 BINDING SITE FOR RESIDUE IM1 B 400 B IM1 400 Software 16 A ASP 29 A ASP 29 2 1_555 B ASP 29 B ASP 29 2 1_555 A ARG 8 A ARG 8 16 1_555 A ASP 25 A ASP 25 16 1_555 A GLY 27 A GLY 27 16 1_555 A ALA 28 A ALA 28 16 1_555 A ASP 29 A ASP 29 16 1_555 A GLY 48 A GLY 48 16 1_555 A GLY 49 A GLY 49 16 1_555 A VAL 82 A VAL 82 16 1_555 B ASP 25 B ASP 25 16 1_555 B GLY 27 B GLY 27 16 1_555 B ALA 28 B ALA 28 16 1_555 B ASP 29 B ASP 29 16 1_555 B GLY 48 B GLY 48 16 1_555 B GLY 49 B GLY 49 16 1_555 B ILE 50 B ILE 50 16 1_555 B HOH 525 E HOH 16 1_555 169 P 61