0.015924 0.009193 0.000000 0.000000 0.018387 0.000000 0.000000 0.000000 0.011976 0.00000 0.00000 0.00000 Chang, C.-H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 62.800 62.800 83.500 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 O3 S 137.158 n S-HYDROXYCYSTEINE L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C33 H36 N4 O3 536.664 [4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-1,3-BIS([(3-AMINO)PHENYL]METHYL)-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPINONE DMP450(INHIBITOR OF DUPONT MERCK) non-polymer 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 C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking 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 UK Chem.Biol. CBOLE2 2050 1074-5521 3 301 314 10.1016/S1074-5521(96)90110-6 8807858 Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450. 1996 10.2210/pdb1dmp/pdb pdb_00001dmp 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 x-ray 1 1.0 COMPLEX WITH DMP450 OF DUPONT MERCK 10773.664 HIV-1 PROTEASE 3.4.23.16 2 man polymer 536.664 [4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-1,3-BIS([(3-AMINO)PHENYL]METHYL)-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPINONE 1 syn non-polymer no yes PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEI(CSO)GHKAIGTVL VGPTPVNIIGRNLLTQIGATLNF PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGATLNF 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 BH102 ISOLATE Escherichia sample 11676 Human immunodeficiency virus 1 562 Escherichia coli 2.20 44.0 5.4 pH 5.4 pdbx_database_status struct_conf struct_conf_type database_2 pdbx_initial_refinement_model struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Derived calculations Other Database references Derived calculations Refinement description 1 0 1997-11-12 1 1 2008-03-03 1 2 2011-07-13 1 3 2017-11-29 1 4 2023-08-09 _pdbx_database_status.process_site _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _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 1996-11-01 REL DMQ [4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-1,3-BIS([(3-AMINO)PHENYL]METHYL)-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPINONE 1HVR PDB ENTRY 1HVR PDB experimental model 450 450 2 DMQ DMQ 450 B PRO 1 n 1 PRO 1 A GLN 2 n 2 GLN 2 A VAL 3 n 3 VAL 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 THR 31 n 31 THR 31 A VAL 32 n 32 VAL 32 A LEU 33 n 33 LEU 33 A GLU 34 n 34 GLU 34 A GLU 35 n 35 GLU 35 A MET 36 n 36 MET 36 A SER 37 n 37 SER 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 CSO 67 n 67 CSO 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 ALA 95 n 95 ALA 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 VAL 3 n 3 VAL 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 THR 31 n 31 THR 31 B VAL 32 n 32 VAL 32 B LEU 33 n 33 LEU 33 B GLU 34 n 34 GLU 34 B GLU 35 n 35 GLU 35 B MET 36 n 36 MET 36 B SER 37 n 37 SER 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 CSO 67 n 67 CSO 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 ALA 95 n 95 ALA 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 4770 -31 8950 A CSO 67 S-HYDROXYCYSTEINE A CSO 67 CYS B CSO 67 S-HYDROXYCYSTEINE B CSO 67 CYS 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 1 B ARG 41 0.110 SIDE CHAIN 1 B ARG 57 0.085 SIDE CHAIN 1 -12.43 2.00 110.40 97.97 A A A CB CA C MET MET MET 36 36 36 N 1 -19.11 3.00 112.40 93.29 A A A CB CG SD MET MET MET 36 36 36 N 1 -3.86 0.60 121.00 117.14 A A A CB CG CD2 TYR TYR TYR 59 59 59 N 1 -11.79 1.80 110.60 98.81 B B B N CA CB ASP ASP ASP 25 25 25 N 1 10.29 1.40 112.40 122.69 B B B CA CB CG2 THR THR THR 91 91 91 N 1 12.34 1.90 110.20 122.54 B B B CB CA C LEU LEU LEU 97 97 97 N 1 A A CE2 CD2 TRP TRP 6 6 0.081 0.012 1.409 1.490 N 1 A A CE2 CD2 TRP TRP 42 42 0.094 0.012 1.409 1.503 N 1 B B CE2 CD2 TRP TRP 6 6 0.087 0.012 1.409 1.496 N 1 A GLU 35 -31.36 131.30 1 A ARG 41 74.71 73.49 1 A CSO 67 38.06 -154.84 1 B GLU 34 -55.24 172.96 1 B CSO 67 43.42 -160.89 0.2100000 0.2100000 2.0 8433 1 PDB ENTRY 1HVR 2.0 0 1884 40 0 1844 0.018 3.8 2.0 1DMP 12478 0.0710000 1 94.0 model building X-PLOR refinement X-PLOR phasing X-PLOR STRUCTURE OF HIV-1 PROTEASE COMPLEX 1 N N 1 N N 2 N N A GLY 86 A GLY 86 HELX_P A GLY 94 A GLY 94 1 HA 9 B GLY 86 B GLY 86 HELX_P B GLY 94 B GLY 94 1 HB 9 covale 1.321 both A ILE 66 A C ILE 66 1_555 A CSO 67 A N CSO 67 1_555 covale 1.340 both A CSO 67 A C CSO 67 1_555 A GLY 68 A N GLY 68 1_555 covale 1.334 both B ILE 66 B C ILE 66 1_555 B CSO 67 B N CSO 67 1_555 covale 1.332 both B CSO 67 B C CSO 67 1_555 B GLY 68 B N GLY 68 1_555 ASPARTYL PROTEINASE AIDS, POLYPROTEIN, HYDROLASE, ASPARTYL PROTEASE, ACID PROTEASE, RNA-DIRECTED DNA POLYMERASE, ENDONUCLEASE, ASPARTYL PROTEINASE A GLY 40 A GLY 40 1 A ARG 41 A ARG 41 27.24 POL_HV1H2 UNP 1 1 P04585 FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQVTLWQRPLVTIKIGGQLKEALL DTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPI ETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQ DFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMT KILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIV LPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDL IAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEY WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA LQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGI DKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIE AEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQV RDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNPLWKGPAKLLWKG EGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED 57 155 1DMP 1 99 P04585 A 1 1 99 57 155 1DMP 1 99 P04585 B 1 1 99 1 CYS modified residue CSO 67 1DMP A P04585 UNP 123 67 1 CYS conflict ALA 95 1DMP A P04585 UNP 151 95 2 CYS modified residue CSO 67 1DMP B P04585 UNP 123 67 2 CYS conflict ALA 95 1DMP B P04585 UNP 151 95 8 8 4 anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A LYS 43 A LYS 43 A GLY 49 A GLY 49 A GLY 52 A GLY 52 A ILE 66 A ILE 66 A HIS 69 A HIS 69 A GLY 78 A GLY 78 A THR 31 A THR 31 A GLU 34 A GLU 34 A ASN 83 A ASN 83 A ILE 85 A ILE 85 A GLN 18 A GLN 18 A ASP 25 A ASP 25 A PRO 9 A PRO 9 A ILE 15 A ILE 15 A GLU 65 A GLU 65 A ILE 66 A ILE 66 B LYS 43 B LYS 43 B GLY 49 B GLY 49 B GLY 52 B GLY 52 B ILE 66 B ILE 66 B HIS 69 B HIS 69 B GLY 78 B GLY 78 B THR 31 B THR 31 B GLU 34 B GLU 34 B ASN 83 B ASN 83 B ILE 85 B ILE 85 B GLN 18 B GLN 18 B ASP 25 B ASP 25 B PRO 9 B PRO 9 B ILE 15 B ILE 15 B GLU 65 B GLU 65 B ILE 66 B ILE 66 A PRO 1 A PRO 1 A THR 4 A THR 4 B THR 96 B THR 96 B PHE 99 B PHE 99 A THR 96 A THR 96 A PHE 99 A PHE 99 B PRO 1 B PRO 1 B THR 4 B THR 4 BINDING SITE FOR RESIDUE DMQ B 450 B DMQ 450 Software 20 A ARG 8 A ARG 8 20 1_555 A ASP 25 A ASP 25 20 1_555 A GLY 27 A GLY 27 20 1_555 A ASP 30 A ASP 30 20 1_555 A VAL 32 A VAL 32 20 1_555 A GLY 48 A GLY 48 20 1_555 A GLY 49 A GLY 49 20 1_555 A ILE 50 A ILE 50 20 1_555 A PRO 81 A PRO 81 20 1_555 A VAL 82 A VAL 82 20 1_555 B ARG 8 B ARG 8 20 1_555 B ASP 25 B ASP 25 20 1_555 B GLY 27 B GLY 27 20 1_555 B ALA 28 B ALA 28 20 1_555 B ASP 29 B ASP 29 20 1_555 B ASP 30 B ASP 30 20 1_555 B ILE 47 B ILE 47 20 1_555 B GLY 49 B GLY 49 20 1_555 B ILE 50 B ILE 50 20 1_555 B ILE 84 B ILE 84 20 1_555 169 P 61