0.026596 0.000000 0.003833 0.000000 0.015773 0.000000 0.000000 0.000000 0.011201 0.00000 0.00000 0.00000 EIGHT ATOMS HAVE BEEN ASSIGNED ZERO OCCUPANCY IN THE FINAL MODEL. THEY ARE ATOMS CG, CD, OE1, AND OE2 OF RESIDUE GLU B 1 AND ATOMS CG, CD, OE1, AND NE2 OF RESIDUE GLN C 3. RESIDUES 8 AND 95 IN CHAINS A AND C ARE CIS PROLINES. Eigenbrot, C. Randal, M. Kossiakoff, A.A. Presta, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 98.20 90.00 37.600 63.400 90.200 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 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 J.Mol.Biol. JMOBAK 0070 0022-2836 229 969 995 10.1006/jmbi.1993.1099 8095303 X-ray structures of the antigen-binding domains from three variants of humanized anti-p185HER2 antibody 4D5 and comparison with molecular modeling. 1993 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 89 4285 Humanization of an Anti-P185-Her2 Antibody for Human Cancer Therapy 1992 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 11964.308 IGG1-KAPPA 4D5 FV (LIGHT CHAIN) 2 man polymer 13176.638 IGG1-KAPPA 4D5 FV (HEAVY CHAIN) 2 man polymer 18.015 water 126 nat water no no DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQP EDFATYYCQQHYTTPPTFGQGTKVEIKRT DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQP EDFATYYCQQHYTTPPTFGQGTKVEIKRT A,C polypeptide(L) no no EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAY LQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAY LQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS B,D 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 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 n n n human sample 9606 Homo sapiens 562 Escherichia coli human sample 9606 Homo sapiens 562 Escherichia coli 2.12 41.86 pdbx_database_status pdbx_unobs_or_zero_occ_atoms struct_conf struct_conf_type repository Initial release Version format compliance Version format compliance Advisory Derived calculations Other 1 0 1993-10-31 1 1 2008-03-24 1 2 2011-07-13 1 3 2017-11-29 _pdbx_database_status.process_site Y BNL 1992-10-20 REL REL HOH water THE RESIDUE NUMBERING IS SEQUENTIAL WITHIN EACH CHAIN. THE SEQUENTIAL NUMBERING OF THE LIGHT CHAIN CORRESPONDS TO THE KABAT NUMBERING SCHEME. THE FOLLOWING IS THE RELATIONSHIP OF THE SEQUENTIAL NUMBERING SCHEME OF THE HEAVY CHAIN TO THE KABAT NUMBERING SCHEME: ENTRY KABAT 1-52 1-52 53 52A 54-83 53-82 84-86 82A,82B,82C 87-104 83-100 105-107 100A,100B,100C 108-120 101-113 HOH 3 3 HOH HOH 110 A HOH 4 3 HOH HOH 111 A HOH 6 3 HOH HOH 112 A HOH 7 3 HOH HOH 113 A HOH 16 3 HOH HOH 114 A HOH 26 3 HOH HOH 115 A HOH 31 3 HOH HOH 116 A HOH 34 3 HOH HOH 117 A HOH 35 3 HOH HOH 118 A HOH 52 3 HOH HOH 119 A HOH 55 3 HOH HOH 120 A HOH 59 3 HOH HOH 121 A HOH 90 3 HOH HOH 122 A HOH 91 3 HOH HOH 123 A HOH 92 3 HOH HOH 124 A HOH 94 3 HOH HOH 125 A HOH 95 3 HOH HOH 126 A HOH 96 3 HOH HOH 127 A HOH 99 3 HOH HOH 128 A HOH 101 3 HOH HOH 129 A HOH 105 3 HOH HOH 130 A HOH 109 3 HOH HOH 131 A HOH 112 3 HOH HOH 132 A HOH 113 3 HOH HOH 133 A HOH 115 3 HOH HOH 134 A HOH 118 3 HOH HOH 135 A HOH 131 3 HOH HOH 136 A HOH 136 3 HOH HOH 137 A HOH 145 3 HOH HOH 138 A HOH 162 3 HOH HOH 139 A HOH 164 3 HOH HOH 140 A HOH 169 3 HOH HOH 141 A HOH 181 3 HOH HOH 142 A HOH 210 3 HOH HOH 143 A HOH 211 3 HOH HOH 144 A HOH 219 3 HOH HOH 145 A HOH 224 3 HOH HOH 146 A HOH 229 3 HOH HOH 147 A HOH 230 3 HOH HOH 148 A HOH 233 3 HOH HOH 149 A HOH 235 3 HOH HOH 150 A HOH 240 3 HOH HOH 151 A HOH 255 3 HOH HOH 152 A HOH 257 3 HOH HOH 153 A HOH 263 3 HOH HOH 154 A HOH 272 3 HOH HOH 155 A HOH 273 3 HOH HOH 156 A HOH 11 3 HOH HOH 121 B HOH 17 3 HOH HOH 122 B HOH 23 3 HOH HOH 123 B HOH 28 3 HOH HOH 124 B HOH 60 3 HOH HOH 125 B HOH 104 3 HOH HOH 126 B HOH 110 3 HOH HOH 127 B HOH 117 3 HOH HOH 128 B HOH 121 3 HOH HOH 129 B HOH 122 3 HOH HOH 130 B HOH 146 3 HOH HOH 131 B HOH 148 3 HOH HOH 132 B HOH 183 3 HOH HOH 133 B HOH 188 3 HOH HOH 134 B HOH 193 3 HOH HOH 135 B HOH 201 3 HOH HOH 136 B HOH 214 3 HOH HOH 137 B HOH 222 3 HOH HOH 138 B HOH 228 3 HOH HOH 139 B HOH 232 3 HOH HOH 140 B HOH 236 3 HOH HOH 141 B HOH 269 3 HOH HOH 142 B HOH 270 3 HOH HOH 143 B HOH 1 3 HOH HOH 110 C HOH 2 3 HOH HOH 111 C HOH 13 3 HOH HOH 112 C HOH 15 3 HOH HOH 113 C HOH 22 3 HOH HOH 114 C HOH 29 3 HOH HOH 115 C HOH 32 3 HOH HOH 116 C HOH 40 3 HOH HOH 117 C HOH 54 3 HOH HOH 118 C HOH 56 3 HOH HOH 119 C HOH 57 3 HOH HOH 120 C HOH 61 3 HOH HOH 121 C HOH 98 3 HOH HOH 122 C HOH 100 3 HOH HOH 123 C HOH 114 3 HOH HOH 124 C HOH 132 3 HOH HOH 125 C HOH 138 3 HOH HOH 126 C HOH 139 3 HOH HOH 127 C HOH 140 3 HOH HOH 128 C HOH 161 3 HOH HOH 129 C HOH 166 3 HOH HOH 130 C HOH 173 3 HOH HOH 131 C HOH 182 3 HOH HOH 132 C HOH 192 3 HOH HOH 133 C HOH 213 3 HOH HOH 134 C HOH 216 3 HOH HOH 135 C HOH 227 3 HOH HOH 136 C HOH 239 3 HOH HOH 137 C HOH 251 3 HOH HOH 138 C HOH 252 3 HOH HOH 139 C HOH 256 3 HOH HOH 140 C HOH 9 3 HOH HOH 121 D HOH 20 3 HOH HOH 122 D HOH 41 3 HOH HOH 123 D HOH 51 3 HOH HOH 124 D HOH 65 3 HOH HOH 125 D HOH 71 3 HOH HOH 126 D HOH 81 3 HOH HOH 127 D HOH 106 3 HOH HOH 128 D HOH 111 3 HOH HOH 129 D HOH 130 3 HOH HOH 130 D HOH 133 3 HOH HOH 131 D HOH 134 3 HOH HOH 132 D HOH 143 3 HOH HOH 133 D HOH 147 3 HOH HOH 134 D HOH 160 3 HOH HOH 135 D HOH 184 3 HOH HOH 136 D HOH 198 3 HOH HOH 137 D HOH 217 3 HOH HOH 138 D HOH 218 3 HOH HOH 139 D HOH 221 3 HOH HOH 140 D HOH 250 3 HOH HOH 141 D HOH 253 3 HOH HOH 142 D HOH 254 3 HOH HOH 143 D HOH 264 3 HOH HOH 144 D HOH 268 3 HOH HOH 145 D ASP 1 n 1 ASP 1 A ILE 2 n 2 ILE 2 A GLN 3 n 3 GLN 3 A MET 4 n 4 MET 4 A THR 5 n 5 THR 5 A GLN 6 n 6 GLN 6 A SER 7 n 7 SER 7 A PRO 8 n 8 PRO 8 A SER 9 n 9 SER 9 A SER 10 n 10 SER 10 A LEU 11 n 11 LEU 11 A SER 12 n 12 SER 12 A ALA 13 n 13 ALA 13 A SER 14 n 14 SER 14 A VAL 15 n 15 VAL 15 A GLY 16 n 16 GLY 16 A ASP 17 n 17 ASP 17 A ARG 18 n 18 ARG 18 A VAL 19 n 19 VAL 19 A THR 20 n 20 THR 20 A ILE 21 n 21 ILE 21 A THR 22 n 22 THR 22 A CYS 23 n 23 CYS 23 A ARG 24 n 24 ARG 24 A ALA 25 n 25 ALA 25 A SER 26 n 26 SER 26 A GLN 27 n 27 GLN 27 A ASP 28 n 28 ASP 28 A VAL 29 n 29 VAL 29 A ASN 30 n 30 ASN 30 A THR 31 n 31 THR 31 A ALA 32 n 32 ALA 32 A VAL 33 n 33 VAL 33 A ALA 34 n 34 ALA 34 A TRP 35 n 35 TRP 35 A TYR 36 n 36 TYR 36 A GLN 37 n 37 GLN 37 A GLN 38 n 38 GLN 38 A LYS 39 n 39 LYS 39 A PRO 40 n 40 PRO 40 A GLY 41 n 41 GLY 41 A LYS 42 n 42 LYS 42 A ALA 43 n 43 ALA 43 A PRO 44 n 44 PRO 44 A LYS 45 n 45 LYS 45 A LEU 46 n 46 LEU 46 A LEU 47 n 47 LEU 47 A ILE 48 n 48 ILE 48 A TYR 49 n 49 TYR 49 A SER 50 n 50 SER 50 A ALA 51 n 51 ALA 51 A SER 52 n 52 SER 52 A PHE 53 n 53 PHE 53 A LEU 54 n 54 LEU 54 A TYR 55 n 55 TYR 55 A SER 56 n 56 SER 56 A GLY 57 n 57 GLY 57 A VAL 58 n 58 VAL 58 A PRO 59 n 59 PRO 59 A SER 60 n 60 SER 60 A ARG 61 n 61 ARG 61 A PHE 62 n 62 PHE 62 A SER 63 n 63 SER 63 A GLY 64 n 64 GLY 64 A SER 65 n 65 SER 65 A ARG 66 n 66 ARG 66 A SER 67 n 67 SER 67 A GLY 68 n 68 GLY 68 A THR 69 n 69 THR 69 A ASP 70 n 70 ASP 70 A PHE 71 n 71 PHE 71 A THR 72 n 72 THR 72 A LEU 73 n 73 LEU 73 A THR 74 n 74 THR 74 A ILE 75 n 75 ILE 75 A SER 76 n 76 SER 76 A SER 77 n 77 SER 77 A LEU 78 n 78 LEU 78 A GLN 79 n 79 GLN 79 A PRO 80 n 80 PRO 80 A GLU 81 n 81 GLU 81 A ASP 82 n 82 ASP 82 A PHE 83 n 83 PHE 83 A ALA 84 n 84 ALA 84 A THR 85 n 85 THR 85 A TYR 86 n 86 TYR 86 A TYR 87 n 87 TYR 87 A CYS 88 n 88 CYS 88 A GLN 89 n 89 GLN 89 A GLN 90 n 90 GLN 90 A HIS 91 n 91 HIS 91 A TYR 92 n 92 TYR 92 A THR 93 n 93 THR 93 A THR 94 n 94 THR 94 A PRO 95 n 95 PRO 95 A PRO 96 n 96 PRO 96 A THR 97 n 97 THR 97 A PHE 98 n 98 PHE 98 A GLY 99 n 99 GLY 99 A GLN 100 n 100 GLN 100 A GLY 101 n 101 GLY 101 A THR 102 n 102 THR 102 A LYS 103 n 103 LYS 103 A VAL 104 n 104 VAL 104 A GLU 105 n 105 GLU 105 A ILE 106 n 106 ILE 106 A LYS 107 n 107 LYS 107 A ARG 108 n 108 ARG 108 A THR 109 n 109 THR 109 A GLU 1 n 1 GLU 1 B VAL 2 n 2 VAL 2 B GLN 3 n 3 GLN 3 B LEU 4 n 4 LEU 4 B VAL 5 n 5 VAL 5 B GLU 6 n 6 GLU 6 B SER 7 n 7 SER 7 B GLY 8 n 8 GLY 8 B GLY 9 n 9 GLY 9 B GLY 10 n 10 GLY 10 B LEU 11 n 11 LEU 11 B VAL 12 n 12 VAL 12 B GLN 13 n 13 GLN 13 B PRO 14 n 14 PRO 14 B GLY 15 n 15 GLY 15 B GLY 16 n 16 GLY 16 B SER 17 n 17 SER 17 B LEU 18 n 18 LEU 18 B ARG 19 n 19 ARG 19 B LEU 20 n 20 LEU 20 B SER 21 n 21 SER 21 B CYS 22 n 22 CYS 22 B ALA 23 n 23 ALA 23 B ALA 24 n 24 ALA 24 B SER 25 n 25 SER 25 B GLY 26 n 26 GLY 26 B PHE 27 n 27 PHE 27 B ASN 28 n 28 ASN 28 B ILE 29 n 29 ILE 29 B LYS 30 n 30 LYS 30 B ASP 31 n 31 ASP 31 B THR 32 n 32 THR 32 B TYR 33 n 33 TYR 33 B ILE 34 n 34 ILE 34 B HIS 35 n 35 HIS 35 B TRP 36 n 36 TRP 36 B VAL 37 n 37 VAL 37 B ARG 38 n 38 ARG 38 B GLN 39 n 39 GLN 39 B ALA 40 n 40 ALA 40 B PRO 41 n 41 PRO 41 B GLY 42 n 42 GLY 42 B LYS 43 n 43 LYS 43 B GLY 44 n 44 GLY 44 B LEU 45 n 45 LEU 45 B GLU 46 n 46 GLU 46 B TRP 47 n 47 TRP 47 B VAL 48 n 48 VAL 48 B ALA 49 n 49 ALA 49 B ARG 50 n 50 ARG 50 B ILE 51 n 51 ILE 51 B TYR 52 n 52 TYR 52 B PRO 53 n 53 PRO 53 B THR 54 n 54 THR 54 B ASN 55 n 55 ASN 55 B GLY 56 n 56 GLY 56 B TYR 57 n 57 TYR 57 B THR 58 n 58 THR 58 B ARG 59 n 59 ARG 59 B TYR 60 n 60 TYR 60 B ALA 61 n 61 ALA 61 B ASP 62 n 62 ASP 62 B SER 63 n 63 SER 63 B VAL 64 n 64 VAL 64 B LYS 65 n 65 LYS 65 B GLY 66 n 66 GLY 66 B ARG 67 n 67 ARG 67 B PHE 68 n 68 PHE 68 B THR 69 n 69 THR 69 B ILE 70 n 70 ILE 70 B SER 71 n 71 SER 71 B ALA 72 n 72 ALA 72 B ASP 73 n 73 ASP 73 B THR 74 n 74 THR 74 B SER 75 n 75 SER 75 B LYS 76 n 76 LYS 76 B ASN 77 n 77 ASN 77 B THR 78 n 78 THR 78 B ALA 79 n 79 ALA 79 B TYR 80 n 80 TYR 80 B LEU 81 n 81 LEU 81 B GLN 82 n 82 GLN 82 B MET 83 n 83 MET 83 B ASN 84 n 84 ASN 84 B SER 85 n 85 SER 85 B LEU 86 n 86 LEU 86 B ARG 87 n 87 ARG 87 B ALA 88 n 88 ALA 88 B GLU 89 n 89 GLU 89 B ASP 90 n 90 ASP 90 B THR 91 n 91 THR 91 B ALA 92 n 92 ALA 92 B VAL 93 n 93 VAL 93 B TYR 94 n 94 TYR 94 B TYR 95 n 95 TYR 95 B CYS 96 n 96 CYS 96 B SER 97 n 97 SER 97 B ARG 98 n 98 ARG 98 B TRP 99 n 99 TRP 99 B GLY 100 n 100 GLY 100 B GLY 101 n 101 GLY 101 B ASP 102 n 102 ASP 102 B GLY 103 n 103 GLY 103 B PHE 104 n 104 PHE 104 B TYR 105 n 105 TYR 105 B ALA 106 n 106 ALA 106 B MET 107 n 107 MET 107 B ASP 108 n 108 ASP 108 B TYR 109 n 109 TYR 109 B TRP 110 n 110 TRP 110 B GLY 111 n 111 GLY 111 B GLN 112 n 112 GLN 112 B GLY 113 n 113 GLY 113 B THR 114 n 114 THR 114 B LEU 115 n 115 LEU 115 B VAL 116 n 116 VAL 116 B THR 117 n 117 THR 117 B VAL 118 n 118 VAL 118 B SER 119 n 119 SER 119 B SER 120 n 120 SER 120 B ASP 1 n 1 ASP 1 C ILE 2 n 2 ILE 2 C GLN 3 n 3 GLN 3 C MET 4 n 4 MET 4 C THR 5 n 5 THR 5 C GLN 6 n 6 GLN 6 C SER 7 n 7 SER 7 C PRO 8 n 8 PRO 8 C SER 9 n 9 SER 9 C SER 10 n 10 SER 10 C LEU 11 n 11 LEU 11 C SER 12 n 12 SER 12 C ALA 13 n 13 ALA 13 C SER 14 n 14 SER 14 C VAL 15 n 15 VAL 15 C GLY 16 n 16 GLY 16 C ASP 17 n 17 ASP 17 C ARG 18 n 18 ARG 18 C VAL 19 n 19 VAL 19 C THR 20 n 20 THR 20 C ILE 21 n 21 ILE 21 C THR 22 n 22 THR 22 C CYS 23 n 23 CYS 23 C ARG 24 n 24 ARG 24 C ALA 25 n 25 ALA 25 C SER 26 n 26 SER 26 C GLN 27 n 27 GLN 27 C ASP 28 n 28 ASP 28 C VAL 29 n 29 VAL 29 C ASN 30 n 30 ASN 30 C THR 31 n 31 THR 31 C ALA 32 n 32 ALA 32 C VAL 33 n 33 VAL 33 C ALA 34 n 34 ALA 34 C TRP 35 n 35 TRP 35 C TYR 36 n 36 TYR 36 C GLN 37 n 37 GLN 37 C GLN 38 n 38 GLN 38 C LYS 39 n 39 LYS 39 C PRO 40 n 40 PRO 40 C GLY 41 n 41 GLY 41 C LYS 42 n 42 LYS 42 C ALA 43 n 43 ALA 43 C PRO 44 n 44 PRO 44 C LYS 45 n 45 LYS 45 C LEU 46 n 46 LEU 46 C LEU 47 n 47 LEU 47 C ILE 48 n 48 ILE 48 C TYR 49 n 49 TYR 49 C SER 50 n 50 SER 50 C ALA 51 n 51 ALA 51 C SER 52 n 52 SER 52 C PHE 53 n 53 PHE 53 C LEU 54 n 54 LEU 54 C TYR 55 n 55 TYR 55 C SER 56 n 56 SER 56 C GLY 57 n 57 GLY 57 C VAL 58 n 58 VAL 58 C PRO 59 n 59 PRO 59 C SER 60 n 60 SER 60 C ARG 61 n 61 ARG 61 C PHE 62 n 62 PHE 62 C SER 63 n 63 SER 63 C GLY 64 n 64 GLY 64 C SER 65 n 65 SER 65 C ARG 66 n 66 ARG 66 C SER 67 n 67 SER 67 C GLY 68 n 68 GLY 68 C THR 69 n 69 THR 69 C ASP 70 n 70 ASP 70 C PHE 71 n 71 PHE 71 C THR 72 n 72 THR 72 C LEU 73 n 73 LEU 73 C THR 74 n 74 THR 74 C ILE 75 n 75 ILE 75 C SER 76 n 76 SER 76 C SER 77 n 77 SER 77 C LEU 78 n 78 LEU 78 C GLN 79 n 79 GLN 79 C PRO 80 n 80 PRO 80 C GLU 81 n 81 GLU 81 C ASP 82 n 82 ASP 82 C PHE 83 n 83 PHE 83 C ALA 84 n 84 ALA 84 C THR 85 n 85 THR 85 C TYR 86 n 86 TYR 86 C TYR 87 n 87 TYR 87 C CYS 88 n 88 CYS 88 C GLN 89 n 89 GLN 89 C GLN 90 n 90 GLN 90 C HIS 91 n 91 HIS 91 C TYR 92 n 92 TYR 92 C THR 93 n 93 THR 93 C THR 94 n 94 THR 94 C PRO 95 n 95 PRO 95 C PRO 96 n 96 PRO 96 C THR 97 n 97 THR 97 C PHE 98 n 98 PHE 98 C GLY 99 n 99 GLY 99 C GLN 100 n 100 GLN 100 C GLY 101 n 101 GLY 101 C THR 102 n 102 THR 102 C LYS 103 n 103 LYS 103 C VAL 104 n 104 VAL 104 C GLU 105 n 105 GLU 105 C ILE 106 n 106 ILE 106 C LYS 107 n 107 LYS 107 C ARG 108 n 108 ARG 108 C n 109 109 C GLU 1 n 1 GLU 1 D VAL 2 n 2 VAL 2 D GLN 3 n 3 GLN 3 D LEU 4 n 4 LEU 4 D VAL 5 n 5 VAL 5 D GLU 6 n 6 GLU 6 D SER 7 n 7 SER 7 D GLY 8 n 8 GLY 8 D GLY 9 n 9 GLY 9 D GLY 10 n 10 GLY 10 D LEU 11 n 11 LEU 11 D VAL 12 n 12 VAL 12 D GLN 13 n 13 GLN 13 D PRO 14 n 14 PRO 14 D GLY 15 n 15 GLY 15 D GLY 16 n 16 GLY 16 D SER 17 n 17 SER 17 D LEU 18 n 18 LEU 18 D ARG 19 n 19 ARG 19 D LEU 20 n 20 LEU 20 D SER 21 n 21 SER 21 D CYS 22 n 22 CYS 22 D ALA 23 n 23 ALA 23 D ALA 24 n 24 ALA 24 D SER 25 n 25 SER 25 D GLY 26 n 26 GLY 26 D PHE 27 n 27 PHE 27 D ASN 28 n 28 ASN 28 D ILE 29 n 29 ILE 29 D LYS 30 n 30 LYS 30 D ASP 31 n 31 ASP 31 D THR 32 n 32 THR 32 D TYR 33 n 33 TYR 33 D ILE 34 n 34 ILE 34 D HIS 35 n 35 HIS 35 D TRP 36 n 36 TRP 36 D VAL 37 n 37 VAL 37 D ARG 38 n 38 ARG 38 D GLN 39 n 39 GLN 39 D ALA 40 n 40 ALA 40 D PRO 41 n 41 PRO 41 D GLY 42 n 42 GLY 42 D LYS 43 n 43 LYS 43 D GLY 44 n 44 GLY 44 D LEU 45 n 45 LEU 45 D GLU 46 n 46 GLU 46 D TRP 47 n 47 TRP 47 D VAL 48 n 48 VAL 48 D ALA 49 n 49 ALA 49 D ARG 50 n 50 ARG 50 D ILE 51 n 51 ILE 51 D TYR 52 n 52 TYR 52 D PRO 53 n 53 PRO 53 D THR 54 n 54 THR 54 D ASN 55 n 55 ASN 55 D GLY 56 n 56 GLY 56 D TYR 57 n 57 TYR 57 D THR 58 n 58 THR 58 D ARG 59 n 59 ARG 59 D TYR 60 n 60 TYR 60 D ALA 61 n 61 ALA 61 D ASP 62 n 62 ASP 62 D SER 63 n 63 SER 63 D VAL 64 n 64 VAL 64 D LYS 65 n 65 LYS 65 D GLY 66 n 66 GLY 66 D ARG 67 n 67 ARG 67 D PHE 68 n 68 PHE 68 D THR 69 n 69 THR 69 D ILE 70 n 70 ILE 70 D SER 71 n 71 SER 71 D ALA 72 n 72 ALA 72 D ASP 73 n 73 ASP 73 D THR 74 n 74 THR 74 D SER 75 n 75 SER 75 D LYS 76 n 76 LYS 76 D ASN 77 n 77 ASN 77 D THR 78 n 78 THR 78 D ALA 79 n 79 ALA 79 D TYR 80 n 80 TYR 80 D LEU 81 n 81 LEU 81 D GLN 82 n 82 GLN 82 D MET 83 n 83 MET 83 D ASN 84 n 84 ASN 84 D SER 85 n 85 SER 85 D LEU 86 n 86 LEU 86 D ARG 87 n 87 ARG 87 D ALA 88 n 88 ALA 88 D GLU 89 n 89 GLU 89 D ASP 90 n 90 ASP 90 D THR 91 n 91 THR 91 D ALA 92 n 92 ALA 92 D VAL 93 n 93 VAL 93 D TYR 94 n 94 TYR 94 D TYR 95 n 95 TYR 95 D CYS 96 n 96 CYS 96 D SER 97 n 97 SER 97 D ARG 98 n 98 ARG 98 D TRP 99 n 99 TRP 99 D GLY 100 n 100 GLY 100 D GLY 101 n 101 GLY 101 D ASP 102 n 102 ASP 102 D GLY 103 n 103 GLY 103 D PHE 104 n 104 PHE 104 D TYR 105 n 105 TYR 105 D ALA 106 n 106 ALA 106 D MET 107 n 107 MET 107 D ASP 108 n 108 ASP 108 D TYR 109 n 109 TYR 109 D TRP 110 n 110 TRP 110 D GLY 111 n 111 GLY 111 D GLN 112 n 112 GLN 112 D GLY 113 n 113 GLY 113 D THR 114 n 114 THR 114 D LEU 115 n 115 LEU 115 D VAL 116 n 116 VAL 116 D THR 117 n 117 THR 117 D VAL 118 n 118 VAL 118 D SER 119 n 119 SER 119 D SER 120 n 120 SER 120 D author_and_software_defined_assembly PISA 2 dimeric author_and_software_defined_assembly PISA 2 dimeric 1480 -12 10220 1430 -12 9860 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 N SER 7 A N SER 7 A O THR 22 A O THR 22 A N CYS 23 A N CYS 23 A O PHE 71 A O PHE 71 A O THR 74 A O THR 74 A N SER 63 A N SER 63 A N LEU 11 A N LEU 11 A O LYS 103 A O LYS 103 A O THR 97 A O THR 97 A N GLN 90 A N GLN 90 A O TYR 87 A O TYR 87 A O TYR 36 A O TYR 36 A O GLN 37 A O GLN 37 A N LYS 45 A N LYS 45 A O ILE 48 A O ILE 48 A N PHE 53 A N PHE 53 B O VAL 5 B O VAL 5 B O ALA 23 B O ALA 23 B O CYS 22 B O CYS 22 B N ALA 79 B N ALA 79 B O TYR 80 B O TYR 80 B N SER 71 B N SER 71 B O GLY 10 B O GLY 10 B N THR 117 B N THR 117 B O THR 114 B O THR 114 B N TYR 94 B N TYR 94 B N SER 97 B N SER 97 B O HIS 35 B O HIS 35 B N TRP 36 B N TRP 36 B O ALA 49 B O ALA 49 B O ARG 50 B O ARG 50 B O ARG 59 B O ARG 59 C O SER 7 C O SER 7 C N THR 22 C N THR 22 C O ILE 21 C O ILE 21 C N LEU 73 C N LEU 73 C N THR 74 C N THR 74 C O SER 63 C O SER 63 C O LEU 11 C O LEU 11 C N GLU 105 C N GLU 105 C O THR 102 C O THR 102 C N TYR 86 C N TYR 86 C O TYR 87 C O TYR 87 C N TYR 36 C N TYR 36 C O VAL 33 C O VAL 33 C N SER 50 C N SER 50 C O TYR 49 C O TYR 49 C N PHE 53 C N PHE 53 D O SER 7 D O SER 7 D N SER 21 D N SER 21 D O LEU 20 D O LEU 20 D N LEU 81 D N LEU 81 D N GLN 82 D N GLN 82 D O THR 69 D O THR 69 D O GLY 10 D O GLY 10 D N THR 117 D N THR 117 D O TYR 109 D O TYR 109 D N ARG 98 D N ARG 98 D O SER 97 D O SER 97 D N HIS 35 D N HIS 35 D O ILE 34 D O ILE 34 D N ILE 51 D N ILE 51 D O VAL 48 D O VAL 48 D N ALA 61 D N ALA 61 1 A CG ARG 108 A CG ARG 108 1 Y 1 A CD ARG 108 A CD ARG 108 1 Y 1 A NE ARG 108 A NE ARG 108 1 Y 1 A CZ ARG 108 A CZ ARG 108 1 Y 1 A NH1 ARG 108 A NH1 ARG 108 1 Y 1 A NH2 ARG 108 A NH2 ARG 108 1 Y 1 C CG ARG 108 C CG ARG 108 1 Y 1 C CD ARG 108 C CD ARG 108 1 Y 1 C NE ARG 108 C NE ARG 108 1 Y 1 C CZ ARG 108 C CZ ARG 108 1 Y 1 C NH1 ARG 108 C NH1 ARG 108 1 Y 1 C NH2 ARG 108 C NH2 ARG 108 1 Y 1 C THR 109 C THR 109 1 Y 1 B TYR 57 0.090 SIDE CHAIN 1 -13.49 2.20 117.20 103.71 A A A CA C N ASP ASP ILE 1 1 2 Y 1 3.90 0.50 120.30 124.20 A A A NE CZ NH1 ARG ARG ARG 18 18 18 N 1 -3.35 0.50 120.30 116.95 A A A NE CZ NH2 ARG ARG ARG 18 18 18 N 1 -12.37 1.80 114.00 101.63 A A A CA CB SG CYS CYS CYS 23 23 23 N 1 8.36 0.80 106.30 114.66 A A A CD1 CG CD2 TRP TRP TRP 35 35 35 N 1 -7.15 1.00 110.10 102.95 A A A CG CD1 NE1 TRP TRP TRP 35 35 35 N 1 -6.68 0.80 107.30 100.62 A A A CE2 CD2 CG TRP TRP TRP 35 35 35 N 1 8.02 0.90 133.90 141.92 A A A CG CD2 CE3 TRP TRP TRP 35 35 35 N 1 3.01 0.50 120.30 123.31 A A A NE CZ NH1 ARG ARG ARG 66 66 66 N 1 -11.98 1.90 110.30 98.32 A A A N CA CB THR THR THR 69 69 69 N 1 -3.67 0.60 121.00 117.33 A A A CB CG CD2 TYR TYR TYR 86 86 86 N 1 3.81 0.50 120.30 124.11 B B B NE CZ NH1 ARG ARG ARG 19 19 19 N 1 -3.25 0.50 120.30 117.05 B B B NE CZ NH2 ARG ARG ARG 19 19 19 N 1 -11.81 1.90 111.00 99.19 B B B CA CB CG1 ILE ILE ILE 29 29 29 N 1 5.55 0.80 106.30 111.85 B B B CD1 CG CD2 TRP TRP TRP 36 36 36 N 1 -5.39 0.80 107.30 101.91 B B B CE2 CD2 CG TRP TRP TRP 36 36 36 N 1 16.31 2.70 111.00 127.31 B B B N CA C LYS LYS LYS 43 43 43 N 1 5.49 0.80 106.30 111.79 B B B CD1 CG CD2 TRP TRP TRP 47 47 47 N 1 -5.89 0.80 107.30 101.41 B B B CE2 CD2 CG TRP TRP TRP 47 47 47 N 1 6.42 0.90 133.90 140.32 B B B CG CD2 CE3 TRP TRP TRP 47 47 47 N 1 -10.55 1.60 110.90 100.35 B B B CG1 CB CG2 VAL VAL VAL 48 48 48 N 1 -4.62 0.60 121.00 116.38 B B B CB CG CD2 TYR TYR TYR 52 52 52 N 1 -3.67 0.60 121.00 117.33 B B B CB CG CD2 TYR TYR TYR 57 57 57 N 1 -15.99 2.20 111.50 95.51 B B B N CA CB VAL VAL VAL 64 64 64 N 1 -5.13 0.60 121.00 115.87 B B B CB CG CD1 TYR TYR TYR 80 80 80 N 1 -13.54 1.60 100.20 86.66 B B B CG SD CE MET MET MET 83 83 83 N 1 3.77 0.50 120.30 124.07 B B B NE CZ NH1 ARG ARG ARG 98 98 98 N 1 -4.01 0.50 120.30 116.29 B B B NE CZ NH2 ARG ARG ARG 98 98 98 N 1 5.49 0.80 106.30 111.79 B B B CD1 CG CD2 TRP TRP TRP 99 99 99 N 1 -4.95 0.80 107.30 102.35 B B B CE2 CD2 CG TRP TRP TRP 99 99 99 N 1 5.30 0.80 106.30 111.60 B B B CD1 CG CD2 TRP TRP TRP 110 110 110 N 1 -4.93 0.80 107.30 102.37 B B B CE2 CD2 CG TRP TRP TRP 110 110 110 N 1 24.33 2.30 115.30 139.63 C C C CA CB CG LEU LEU LEU 11 11 11 N 1 4.26 0.50 120.30 124.56 C C C NE CZ NH1 ARG ARG ARG 24 24 24 N 1 -3.25 0.50 120.30 117.05 C C C NE CZ NH2 ARG ARG ARG 24 24 24 N 1 -14.43 2.20 111.50 97.07 C C C N CA CB VAL VAL VAL 29 29 29 N 1 6.18 0.80 106.30 112.48 C C C CD1 CG CD2 TRP TRP TRP 35 35 35 N 1 -5.80 0.80 107.30 101.50 C C C CE2 CD2 CG TRP TRP TRP 35 35 35 N 1 5.45 0.90 133.90 139.35 C C C CG CD2 CE3 TRP TRP TRP 35 35 35 N 1 -3.70 0.60 121.00 117.30 C C C CB CG CD2 TYR TYR TYR 49 49 49 N 1 13.30 2.20 117.20 130.50 C C C CA C N GLY GLY VAL 57 57 58 Y 1 -4.39 0.60 121.00 116.61 C C C CB CG CD2 TYR TYR TYR 92 92 92 N 1 -4.28 0.60 121.00 116.72 D D D CB CG CD2 TYR TYR TYR 33 33 33 N 1 3.58 0.50 120.30 123.88 D D D NE CZ NH1 ARG ARG ARG 38 38 38 N 1 7.23 0.80 106.30 113.53 D D D CD1 CG CD2 TRP TRP TRP 47 47 47 N 1 -6.71 1.00 110.10 103.39 D D D CG CD1 NE1 TRP TRP TRP 47 47 47 N 1 -5.12 0.80 107.30 102.18 D D D CE2 CD2 CG TRP TRP TRP 47 47 47 N 1 -5.77 0.60 121.00 115.23 D D D CB CG CD2 TYR TYR TYR 57 57 57 N 1 4.32 0.50 120.30 124.62 D D D NE CZ NH1 ARG ARG ARG 59 59 59 N 1 -4.09 0.60 121.00 116.91 D D D CB CG CD1 TYR TYR TYR 60 60 60 N 1 -4.00 0.60 121.00 117.00 D D D CB CG CD2 TYR TYR TYR 80 80 80 N 1 5.56 0.80 106.30 111.86 D D D CD1 CG CD2 TRP TRP TRP 99 99 99 N 1 -5.07 0.80 107.30 102.23 D D D CE2 CD2 CG TRP TRP TRP 99 99 99 N 1 6.21 0.80 106.30 112.51 D D D CD1 CG CD2 TRP TRP TRP 110 110 110 N 1 -7.82 1.30 127.00 119.18 D D D CB CG CD1 TRP TRP TRP 110 110 110 N 1 -6.01 0.80 107.30 101.29 D D D CE2 CD2 CG TRP TRP TRP 110 110 110 N 1 5.91 0.90 133.90 139.81 D D D CG CD2 CE3 TRP TRP TRP 110 110 110 N 1 A A NE2 CD2 HIS HIS 91 91 -0.069 0.011 1.373 1.304 N 1 D D NE2 CD2 HIS HIS 35 35 -0.076 0.011 1.373 1.297 N 1 A ASN 30 67.70 -121.56 1 A ALA 51 54.78 -13.57 1 A SER 52 -157.08 17.85 1 A SER 60 -59.72 -3.67 1 A SER 77 -168.16 94.57 1 B TYR 105 -105.90 42.42 1 C ASN 30 60.04 -126.43 1 C ALA 32 -67.60 65.00 1 C ALA 51 50.13 -22.13 1 C SER 52 -152.09 11.17 1 C ALA 84 -165.39 -168.80 1 D VAL 2 113.04 107.34 1 D ASN 55 -150.97 3.84 1 D ALA 92 178.90 168.94 1 D ASP 102 0.76 117.39 1 D SER 119 -132.09 -50.44 0.183 0.183 2.2 10. 1 2.0 2.2 10. 126 3647 0 0 3521 0.015 3.2 model building X-PLOR refinement X-PLOR phasing X-PLOR FV FRAGMENT OF HUMANIZED ANTIBODY 4D5, VERSION 8 X-RAY STRUCTURES OF THE ANTIGEN-BINDING DOMAINS FROM THREE VARIANTS OF HUMANIZED ANTI-P185-HER2 ANTIBODY 4D5 AND COMPARISON WITH MOLECULAR MODELING 1 N N 2 N N 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. THE LIGHT AND HEAVY CHAINS OF MOLECULE 1 ARE DENOTED BY CHAIN IDENTIFIERS *A* AND *B*. THE LIGHT AND HEAVY CHAINS OF MOLECULE 2 ARE DENOTED BY THE CHAIN IDENTIFIERS *C* AND *D*. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *C* AND *D*. A GLN 79 A GLN 79 HELX_P A PHE 83 A PHE 83 5 1 5 B ARG 87 B ARG 87 HELX_P B THR 91 B THR 91 5 2 5 C GLN 79 C GLN 79 HELX_P C PHE 83 C PHE 83 5 3 5 D ARG 87 D ARG 87 HELX_P D THR 91 D THR 91 5 4 5 disulf 2.001 A CYS 23 A SG CYS 23 1_555 A CYS 88 A SG CYS 88 1_555 disulf 2.017 B CYS 22 B SG CYS 22 1_555 B CYS 96 B SG CYS 96 1_555 disulf 2.003 C CYS 23 C SG CYS 23 1_555 C CYS 88 C SG CYS 88 1_555 disulf 2.004 D CYS 22 D SG CYS 22 1_555 D CYS 96 D SG CYS 96 1_555 IMMUNOGLOBULIN IMMUNOGLOBULIN A SER 7 A SER 7 1 A PRO 8 A PRO 8 -3.19 A THR 94 A THR 94 1 A PRO 95 A PRO 95 -3.61 C SER 7 C SER 7 1 C PRO 8 C PRO 8 -4.03 C THR 94 C THR 94 1 C PRO 95 C PRO 95 -9.95 given -0.997760 0.036730 0.055950 0.037030 -0.999300 -0.004350 0.055760 -0.006410 0.998420 36.96113 27.31182 -0.46846 AAA59089 GB 1 1 185985 MDMRVPAQLLGLLLLWLRGARCDIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGV PSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPWTFGQGTKVEIKRTVAAPSVFIFPPS 1FVC PDB 2 1FVC 23 132 1FVC 1 109 185985 A 1 1 109 23 132 1FVC 1 109 185985 C 1 1 109 1 120 1FVC 1 120 1FVC B 2 1 120 1 120 1FVC 1 120 1FVC D 2 1 120 1 SER CONFLICT ASP 28 1FVC A 185985 GB 50 28 1 ILE CONFLICT VAL 29 1FVC A 185985 GB 51 29 1 SER CONFLICT ASN 30 1FVC A 185985 GB 52 30 1 SER CONFLICT THR 31 1FVC A 185985 GB 53 31 1 TYR CONFLICT ALA 32 1FVC A 185985 GB 54 32 1 LEU CONFLICT VAL 33 1FVC A 185985 GB 55 33 1 ASN CONFLICT ALA 34 1FVC A 185985 GB 56 34 1 ALA CONFLICT SER 50 1FVC A 185985 GB 72 50 1 SER CONFLICT PHE 53 1FVC A 185985 GB 75 53 1 GLN CONFLICT TYR 55 1FVC A 185985 GB 77 55 1 GLY CONFLICT ARG 66 1FVC A 185985 GB 88 66 1 SER CONFLICT HIS 91 1FVC A 185985 GB 113 91 1 SER CONFLICT THR 93 1FVC A 185985 GB 115 93 1 TRP DELETION 1FVC A 185985 GB 119 2 SER CONFLICT ASP 28 1FVC C 185985 GB 50 28 2 ILE CONFLICT VAL 29 1FVC C 185985 GB 51 29 2 SER CONFLICT ASN 30 1FVC C 185985 GB 52 30 2 SER CONFLICT THR 31 1FVC C 185985 GB 53 31 2 TYR CONFLICT ALA 32 1FVC C 185985 GB 54 32 2 LEU CONFLICT VAL 33 1FVC C 185985 GB 55 33 2 ASN CONFLICT ALA 34 1FVC C 185985 GB 56 34 2 ALA CONFLICT SER 50 1FVC C 185985 GB 72 50 2 SER CONFLICT PHE 53 1FVC C 185985 GB 75 53 2 GLN CONFLICT TYR 55 1FVC C 185985 GB 77 55 2 GLY CONFLICT ARG 66 1FVC C 185985 GB 88 66 2 SER CONFLICT HIS 91 1FVC C 185985 GB 113 91 2 SER CONFLICT THR 93 1FVC C 185985 GB 115 93 2 TRP DELETION 1FVC C 185985 GB 119 4 6 4 6 4 6 4 6 anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel A GLN 3 A GLN 3 A SER 7 A SER 7 A VAL 19 A VAL 19 A ALA 25 A ALA 25 A ASP 70 A ASP 70 A ILE 75 A ILE 75 A ARG 61 A ARG 61 A SER 67 A SER 67 A SER 9 A SER 9 A ALA 13 A ALA 13 A THR 97 A THR 97 A GLU 105 A GLU 105 A THR 85 A THR 85 A HIS 91 A HIS 91 A ALA 32 A ALA 32 A GLN 38 A GLN 38 A LYS 45 A LYS 45 A ILE 48 A ILE 48 A PHE 53 A PHE 53 A TYR 55 A TYR 55 B GLN 3 B GLN 3 B SER 7 B SER 7 B GLY 16 B GLY 16 B SER 25 B SER 25 B ASN 77 B ASN 77 B SER 85 B SER 85 B ARG 67 B ARG 67 B ASP 73 B ASP 73 B GLY 10 B GLY 10 B VAL 12 B VAL 12 B TYR 109 B TYR 109 B SER 119 B SER 119 B ALA 92 B ALA 92 B TRP 99 B TRP 99 B TYR 33 B TYR 33 B ARG 38 B ARG 38 B GLU 46 B GLU 46 B TYR 52 B TYR 52 B TYR 57 B TYR 57 B ALA 61 B ALA 61 C GLN 3 C GLN 3 C SER 7 C SER 7 C VAL 19 C VAL 19 C SER 26 C SER 26 C THR 69 C THR 69 C ILE 75 C ILE 75 C ARG 61 C ARG 61 C SER 67 C SER 67 C SER 9 C SER 9 C ALA 13 C ALA 13 C THR 97 C THR 97 C LYS 107 C LYS 107 C ALA 84 C ALA 84 C GLN 90 C GLN 90 C VAL 33 C VAL 33 C GLN 38 C GLN 38 C LEU 47 C LEU 47 C SER 50 C SER 50 C PHE 53 C PHE 53 C TYR 55 C TYR 55 D GLN 3 D GLN 3 D SER 7 D SER 7 D GLY 16 D GLY 16 D SER 25 D SER 25 D ASN 77 D ASN 77 D SER 85 D SER 85 D THR 69 D THR 69 D ASP 73 D ASP 73 D GLY 10 D GLY 10 D VAL 12 D VAL 12 D TYR 109 D TYR 109 D SER 119 D SER 119 D ALA 92 D ALA 92 D ARG 98 D ARG 98 D ILE 34 D ILE 34 D GLN 39 D GLN 39 D GLU 46 D GLU 46 D TYR 52 D TYR 52 D GLY 56 D GLY 56 D ALA 61 D ALA 61 4 P 1 21 1