0.013441 0.007760 0.000000 0.000000 0.015520 0.000000 0.000000 0.000000 0.025773 0.00000 0.00000 0.00000 Holland, D.R. Rubin, J.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 74.400 74.400 38.800 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 C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE 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 C25 H38 N3 O10 P 571.557 4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID non-polymer C5 H11 N O2 117.146 y VALINE L-peptide linking US J.Med.Chem. JMCMAR 0151 0022-2623 40 3719 3725 10.1021/jm970402q 9371236 Design, synthesis, and cocrystal structure of a nonpeptide Src SH2 domain ligand. 1997 US Cell(Cambridge,Mass.) CELLB5 0998 0092-8674 72 779 Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms 1993 10.2210/pdb1skj/pdb pdb_00001skj 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 293 1 IMAGE PLATE 1994-07 MARRESEARCH CU FILTER M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 12907.508 PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN 2.7.1.112 SH2 DOMAIN N-TERMINAL INS(GS) AND C-TERMINAL INS(EFIVTD) 1 man polymer 571.557 4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID 1 syn non-polymer 18.015 water 61 nat water SRC SH2 no no GSAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSS LQQLVAYYSKHADGLCHRLTNVCPTSKEFIVTD GSAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSS LQQLVAYYSKHADGLCHRLTNVCPTSKEFIVTD A 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 n n n n n n n n n n n n n n Alpharetrovirus SCHMIDT-RUPPIN STRAIN A Escherichia sample JM 83 11886 Rous sarcoma virus JM83 562 Escherichia coli PGEX-KT BACTERIUM 1 2.5 48.77 WAKSMAN AND KURIYAN SRC SH2 STRUCTURE VAPOR DIFFUSION, HANGING DROP 6.0 20% PEG 6K, 0.1M ODIUM CACODYLATE PH 6, HANGING DROP EXPERIMENT, PROTEIN 29 MG/ ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 6.0, vapor diffusion - hanging drop database_2 pdbx_database_status pdbx_initial_refinement_model struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Refinement description 1 0 1998-02-25 1 1 2008-03-03 1 2 2011-07-13 1 3 2023-08-09 _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 1997-09-18 REL REL UR2 4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID HOH water G-S-A-A-E- - : G-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING : E-F-I-V-T-D NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING 1SPS PROTEIN MODEL FROM 1SPS PDB experimental model UR2 1 2 UR2 UR2 113 A HOH 1 3 HOH HOH 114 A HOH 2 3 HOH HOH 115 A HOH 3 3 HOH HOH 116 A HOH 4 3 HOH HOH 117 A HOH 5 3 HOH HOH 118 A HOH 7 3 HOH HOH 119 A HOH 9 3 HOH HOH 120 A HOH 10 3 HOH HOH 121 A HOH 11 3 HOH HOH 122 A HOH 12 3 HOH HOH 123 A HOH 13 3 HOH HOH 124 A HOH 16 3 HOH HOH 125 A HOH 19 3 HOH HOH 126 A HOH 21 3 HOH HOH 127 A HOH 22 3 HOH HOH 128 A HOH 23 3 HOH HOH 129 A HOH 24 3 HOH HOH 130 A HOH 25 3 HOH HOH 131 A HOH 26 3 HOH HOH 132 A HOH 27 3 HOH HOH 133 A HOH 28 3 HOH HOH 134 A HOH 30 3 HOH HOH 135 A HOH 31 3 HOH HOH 136 A HOH 32 3 HOH HOH 137 A HOH 33 3 HOH HOH 138 A HOH 36 3 HOH HOH 139 A HOH 37 3 HOH HOH 140 A HOH 38 3 HOH HOH 141 A HOH 39 3 HOH HOH 142 A HOH 40 3 HOH HOH 143 A HOH 41 3 HOH HOH 144 A HOH 42 3 HOH HOH 145 A HOH 44 3 HOH HOH 146 A HOH 45 3 HOH HOH 147 A HOH 48 3 HOH HOH 148 A HOH 49 3 HOH HOH 149 A HOH 51 3 HOH HOH 150 A HOH 52 3 HOH HOH 151 A HOH 53 3 HOH HOH 152 A HOH 55 3 HOH HOH 153 A HOH 60 3 HOH HOH 154 A HOH 63 3 HOH HOH 155 A HOH 65 3 HOH HOH 156 A HOH 67 3 HOH HOH 157 A HOH 68 3 HOH HOH 158 A HOH 69 3 HOH HOH 159 A HOH 71 3 HOH HOH 160 A HOH 74 3 HOH HOH 161 A HOH 77 3 HOH HOH 162 A HOH 80 3 HOH HOH 163 A HOH 85 3 HOH HOH 164 A HOH 88 3 HOH HOH 165 A HOH 89 3 HOH HOH 166 A HOH 93 3 HOH HOH 167 A HOH 94 3 HOH HOH 168 A HOH 96 3 HOH HOH 169 A HOH 97 3 HOH HOH 170 A HOH 98 3 HOH HOH 171 A HOH 106 3 HOH HOH 172 A HOH 116 3 HOH HOH 173 A HOH 117 3 HOH HOH 174 A n 1 0 A n 2 1 A n 3 2 A GLU 3 n 4 GLU 3 A GLU 4 n 5 GLU 4 A TRP 5 n 6 TRP 5 A TYR 6 n 7 TYR 6 A PHE 7 n 8 PHE 7 A GLY 8 n 9 GLY 8 A LYS 9 n 10 LYS 9 A ILE 10 n 11 ILE 10 A THR 11 n 12 THR 11 A ARG 12 n 13 ARG 12 A ARG 13 n 14 ARG 13 A GLU 14 n 15 GLU 14 A SER 15 n 16 SER 15 A GLU 16 n 17 GLU 16 A ARG 17 n 18 ARG 17 A LEU 18 n 19 LEU 18 A LEU 19 n 20 LEU 19 A LEU 20 n 21 LEU 20 A ASN 21 n 22 ASN 21 A PRO 22 n 23 PRO 22 A GLU 23 n 24 GLU 23 A ASN 24 n 25 ASN 24 A PRO 25 n 26 PRO 25 A ARG 26 n 27 ARG 26 A GLY 27 n 28 GLY 27 A THR 28 n 29 THR 28 A PHE 29 n 30 PHE 29 A LEU 30 n 31 LEU 30 A VAL 31 n 32 VAL 31 A ARG 32 n 33 ARG 32 A GLU 33 n 34 GLU 33 A SER 34 n 35 SER 34 A GLU 35 n 36 GLU 35 A THR 36 n 37 THR 36 A THR 37 n 38 THR 37 A LYS 38 n 39 LYS 38 A GLY 39 n 40 GLY 39 A ALA 40 n 41 ALA 40 A TYR 41 n 42 TYR 41 A CYS 42 n 43 CYS 42 A LEU 43 n 44 LEU 43 A SER 44 n 45 SER 44 A VAL 45 n 46 VAL 45 A SER 46 n 47 SER 46 A ASP 47 n 48 ASP 47 A PHE 48 n 49 PHE 48 A ASP 49 n 50 ASP 49 A ASN 50 n 51 ASN 50 A ALA 51 n 52 ALA 51 A LYS 52 n 53 LYS 52 A GLY 53 n 54 GLY 53 A LEU 54 n 55 LEU 54 A ASN 55 n 56 ASN 55 A VAL 56 n 57 VAL 56 A LYS 57 n 58 LYS 57 A HIS 58 n 59 HIS 58 A TYR 59 n 60 TYR 59 A LYS 60 n 61 LYS 60 A ILE 61 n 62 ILE 61 A ARG 62 n 63 ARG 62 A LYS 63 n 64 LYS 63 A LEU 64 n 65 LEU 64 A ASP 65 n 66 ASP 65 A SER 66 n 67 SER 66 A GLY 67 n 68 GLY 67 A GLY 68 n 69 GLY 68 A PHE 69 n 70 PHE 69 A TYR 70 n 71 TYR 70 A ILE 71 n 72 ILE 71 A THR 72 n 73 THR 72 A SER 73 n 74 SER 73 A ARG 74 n 75 ARG 74 A THR 75 n 76 THR 75 A GLN 76 n 77 GLN 76 A PHE 77 n 78 PHE 77 A SER 78 n 79 SER 78 A SER 79 n 80 SER 79 A LEU 80 n 81 LEU 80 A GLN 81 n 82 GLN 81 A GLN 82 n 83 GLN 82 A LEU 83 n 84 LEU 83 A VAL 84 n 85 VAL 84 A ALA 85 n 86 ALA 85 A TYR 86 n 87 TYR 86 A TYR 87 n 88 TYR 87 A SER 88 n 89 SER 88 A LYS 89 n 90 LYS 89 A HIS 90 n 91 HIS 90 A ALA 91 n 92 ALA 91 A ASP 92 n 93 ASP 92 A GLY 93 n 94 GLY 93 A LEU 94 n 95 LEU 94 A CYS 95 n 96 CYS 95 A HIS 96 n 97 HIS 96 A ARG 97 n 98 ARG 97 A LEU 98 n 99 LEU 98 A THR 99 n 100 THR 99 A ASN 100 n 101 ASN 100 A VAL 101 n 102 VAL 101 A CYS 102 n 103 CYS 102 A PRO 103 n 104 PRO 103 A THR 104 n 105 THR 104 A n 106 105 A n 107 106 A n 108 107 A n 109 108 A n 110 109 A n 111 110 A n 112 111 A n 113 112 A author_defined_assembly 1 monomeric 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 LEU 30 A O LEU 31 A N SER 44 A N SER 45 A O TYR 41 A O TYR 42 A N ILE 61 A N ILE 62 1 A CB GLU 3 A CB GLU 4 1 Y 1 A CG GLU 3 A CG GLU 4 1 Y 1 A CD GLU 3 A CD GLU 4 1 Y 1 A OE1 GLU 3 A OE1 GLU 4 1 Y 1 A OE2 GLU 3 A OE2 GLU 4 1 Y 1 A CG GLU 4 A CG GLU 5 1 Y 1 A CD GLU 4 A CD GLU 5 1 Y 1 A OE1 GLU 4 A OE1 GLU 5 1 Y 1 A OE2 GLU 4 A OE2 GLU 5 1 Y 1 A GLY 0 A GLY 1 1 Y 1 A SER 1 A SER 2 1 Y 1 A ALA 2 A ALA 3 1 Y 1 A SER 105 A SER 106 1 Y 1 A LYS 106 A LYS 107 1 Y 1 A GLU 107 A GLU 108 1 Y 1 A PHE 108 A PHE 109 1 Y 1 A ILE 109 A ILE 110 1 Y 1 A VAL 110 A VAL 111 1 Y 1 A THR 111 A THR 112 1 Y 1 A ASP 112 A ASP 113 1 Y 1 A CA THR 104 WRONG HAND 1 A TYR 41 0.070 SIDE CHAIN 1 14.19 2.30 115.30 129.49 A A A CA CB CG LEU LEU LEU 30 30 30 N 1 A GLU 4 -34.37 -30.75 1 A SER 66 -95.70 39.39 1 A THR 99 -117.09 -88.43 17. 0.2750000 0.2000000 0.2000000 2.0 8. 438 4253 10. 89. RANDOM 1 R-FREE 2.4 MOLECULAR REPLACEMENT PROTEIN MODEL FROM 1SPS 2.0 8. 61 881 0 0 820 0.014 2.9 28.6 2.7 0.2800000 0.2400000 2.51 53 445 8 10. 85. 25.5 2.4 25. 1SKJ 4694 2. 0.1090000 1 18.9 3.7 95.48 0.2760000 2.4 2.5 7. 3.5 96.9 model building X-PLOR 3.1 refinement X-PLOR 3.1 data reduction XDS data scaling XDS phasing X-PLOR 3.1 COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX 1 N N 2 N N 3 N N A ARG 12 A ARG 13 HELX_P A LEU 19 A LEU 20 1 1 8 A LEU 80 A LEU 81 HELX_P A TYR 87 A TYR 88 1 2 8 TYROSINE-PROTEIN KINASE TYROSINE-PROTEIN KINASE, V-SRC SH2 DOMAIN, PHOSPHOTYROSINE RECOGNITION DOMAIN, PP60 SRC SH2 DOMAIN, PEPTIDOMIMETIC, UREIDO SRC_RSVSA UNP 1 1 P00524 MGSSKSKPKGPSQRRRSLEPPDSTHHGGFPASQTPNKTAAPDTHRTPSRSFGTVATEPKLFGDFNTSDTVTSPQRAGALA GGVTTFVALYDYESWIETDLSFKKGERLQIVNNTEGNWWLAHSVTTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESER LLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHR LTNVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHK KLVQLYAVVSEEPIYIVIEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVC KVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMGNGEVLDRVERGYR MPCPPECPESLHDLMSQCWRRDPEERPTFEYLQAQLLPACVLEVAE 142 252 1SKJ 1 111 P00524 A 1 2 112 1 ILE deletion 1SKJ A P00524 UNP 143 1 GLN deletion 1SKJ A P00524 UNP 144 1 insertion GLU 107 1SKJ A P00524 UNP 108 1 insertion PHE 108 1SKJ A P00524 UNP 109 1 PRO conflict ILE 109 1SKJ A P00524 UNP 250 110 1 GLN conflict VAL 110 1SKJ A P00524 UNP 251 111 3 anti-parallel anti-parallel A PHE 29 A PHE 30 A GLU 33 A GLU 34 A TYR 41 A TYR 42 A ASP 49 A ASP 50 A GLY 53 A GLY 54 A ILE 61 A ILE 62 BINDING SITE FOR RESIDUE UR2 A 113 A UR2 113 Software 16 A PRO 22 A PRO 23 16 4_674 A ARG 26 A ARG 27 16 4_674 A ARG 32 A ARG 33 16 1_555 A SER 34 A SER 35 16 1_555 A GLU 35 A GLU 36 16 1_555 A THR 36 A THR 37 16 1_555 A CYS 42 A CYS 43 16 1_555 A HIS 58 A HIS 59 16 1_555 A TYR 59 A TYR 60 16 1_555 A LYS 60 A LYS 61 16 1_555 A ILE 71 A ILE 72 16 1_555 A ASP 92 A ASP 93 16 1_555 A GLY 93 A GLY 94 16 1_555 A HIS 96 A HIS 97 16 4_674 A HOH 133 C HOH 16 4_674 A HOH 153 C HOH 16 1_555 169 P 61