0.017182 0.000000 0.000000 0.000000 0.016453 0.000000 0.000000 0.000000 0.030553 0.00000 0.00000 0.00000 Muraki, M. Harata, K. Sugita, N. Sato, K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 58.20 60.78 32.73 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 C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer 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 C8 H15 N O6 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE D-saccharide, beta 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 39 292 299 10.1021/bi991402q 10630988 Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling. 2000 US Biochemistry BICHAW 0033 0006-2960 38 540 548 10.1021/bi981779g Dual Affinity Labeling of the Active Site of Human Lysozyme with an N-Acetyllactosamine Derivative: First Ligand Assisted Recognition of the Second Ligand 1999 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 54 834 843 10.1107/S090744499800122X X-ray Structure of Human Lysozyme Labelled with 2',3'-Epoxypropyl b-Glycoside of Man-b1,4-GlcNAc. Structural Change and Recognition Specificity at Subsite B 1998 US Biochemistry BICHAW 0033 0006-2960 35 13562 13567 10.1021/bi9613180 Origin of Carbohydrate Recognition Specificity of Human Lysozyme Revealed by Affinity Labeling 1996 US Biochemistry BICHAW 0033 0006-2960 31 9212 9219 Dissection of the Functional Role of Structural Elements of Tyrosine-63 in the Catalytic Action of Human Lysozyme 1992 10.2210/pdb1d6p/pdb pdb_00001d6p 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 288.0 1 DIFFRACTOMETER 1999-05-10 ENRAF-NONIUS FAST SINGLE WAVELENGTH M x-ray 1 1.5148 1.0 1.5148 ROTATING ANODE ENRAF-NONIUS FR571 14670.676 LYSOZYME 3.2.1.17 Y63L 1 man polymer 424.401 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 1 man branched 92.094 GLYCEROL 1 syn non-polymer 18.015 water 43 nat water no no KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRLWCNDGKTPGAVNACHLS CSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRLWCNDGKTPGAVNACHLS CSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV 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 n n n n n n n n n n n n n n n n n human Homo sample 9606 Homo sapiens 1 1.97 37.65 VAPOR DIFFUSION, SITTING DROP 4.5 5M NH4NO3 IN 10 MM NAOAC(PH 4.5), VAPOR DIFFUSION, SITTING DROP, temperature 298.0K 298.0 software diffrn_detector atom_site chem_comp entity pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_assembly_gen struct_asym struct_conn struct_site struct_site_gen chem_comp database_2 struct_ref_seq_dif repository Initial release Carbohydrate remediation repository Remediation Version format compliance Non-polymer description Version format compliance Refinement description Data collection Atomic model Data collection Derived calculations Structure summary Database references Structure summary 1 0 2000-01-21 1 1 2007-10-16 1 2 2011-07-13 1 3 2017-10-04 1 4 2018-04-18 2 0 2020-07-29 2 1 2021-11-03 _software.name _diffrn_detector.detector _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.label_asym_id _chem_comp.name _chem_comp.type _entity.formula_weight _entity.pdbx_description _entity.pdbx_number_of_molecules _entity.type _pdbx_struct_assembly_gen.asym_id_list _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details NAG 132 n B NAG 1 NAG 131 n B NAG 2 DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc HUMAN LYSOZYME (WILD TYPE) LABELLED WITH 2',3'-EPOXYPROPYL GLYCOSIDE OF N,N'-DIACETYL CHITOBIOSE HUMAN LYSOZYME D102E MUTANT RCSB Y RCSB 1999-10-15 REL REL oligosaccharide DGlcpNAcb1-4DGlcpNAcb1-ROH 2 GMML 1.0 Glycam Condensed Sequence WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1 2 PDB2Glycan 1.1.0 WURCS [][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}} 2 PDB-CARE LINUCS C1 O4 NAG NAG 2 1 2 O1 HO4 sing n n GOL GLYCEROL HOH water GOL 133 3 GOL GOL 133 A HOH 134 4 HOH HOH 134 A HOH 135 4 HOH HOH 135 A HOH 136 4 HOH HOH 136 A HOH 137 4 HOH HOH 137 A HOH 138 4 HOH HOH 138 A HOH 139 4 HOH HOH 139 A HOH 140 4 HOH HOH 140 A HOH 141 4 HOH HOH 141 A HOH 142 4 HOH HOH 142 A HOH 143 4 HOH HOH 143 A HOH 144 4 HOH HOH 144 A HOH 145 4 HOH HOH 145 A HOH 146 4 HOH HOH 146 A HOH 147 4 HOH HOH 147 A HOH 148 4 HOH HOH 148 A HOH 149 4 HOH HOH 149 A HOH 150 4 HOH HOH 150 A HOH 151 4 HOH HOH 151 A HOH 152 4 HOH HOH 152 A HOH 153 4 HOH HOH 153 A HOH 154 4 HOH HOH 154 A HOH 155 4 HOH HOH 155 A HOH 156 4 HOH HOH 156 A HOH 157 4 HOH HOH 157 A HOH 158 4 HOH HOH 158 A HOH 159 4 HOH HOH 159 A HOH 160 4 HOH HOH 160 A HOH 161 4 HOH HOH 161 A HOH 162 4 HOH HOH 162 A HOH 163 4 HOH HOH 163 A HOH 164 4 HOH HOH 164 A HOH 165 4 HOH HOH 165 A HOH 166 4 HOH HOH 166 A HOH 167 4 HOH HOH 167 A HOH 168 4 HOH HOH 168 A HOH 169 4 HOH HOH 169 A HOH 170 4 HOH HOH 170 A HOH 171 4 HOH HOH 171 A HOH 172 4 HOH HOH 172 A HOH 173 4 HOH HOH 173 A HOH 174 4 HOH HOH 174 A HOH 175 4 HOH HOH 175 A HOH 176 4 HOH HOH 176 A LYS 1 n 1 LYS 1 A VAL 2 n 2 VAL 2 A PHE 3 n 3 PHE 3 A GLU 4 n 4 GLU 4 A ARG 5 n 5 ARG 5 A CYS 6 n 6 CYS 6 A GLU 7 n 7 GLU 7 A LEU 8 n 8 LEU 8 A ALA 9 n 9 ALA 9 A ARG 10 n 10 ARG 10 A THR 11 n 11 THR 11 A LEU 12 n 12 LEU 12 A LYS 13 n 13 LYS 13 A ARG 14 n 14 ARG 14 A LEU 15 n 15 LEU 15 A GLY 16 n 16 GLY 16 A MET 17 n 17 MET 17 A ASP 18 n 18 ASP 18 A GLY 19 n 19 GLY 19 A TYR 20 n 20 TYR 20 A ARG 21 n 21 ARG 21 A GLY 22 n 22 GLY 22 A ILE 23 n 23 ILE 23 A SER 24 n 24 SER 24 A LEU 25 n 25 LEU 25 A ALA 26 n 26 ALA 26 A ASN 27 n 27 ASN 27 A TRP 28 n 28 TRP 28 A MET 29 n 29 MET 29 A CYS 30 n 30 CYS 30 A LEU 31 n 31 LEU 31 A ALA 32 n 32 ALA 32 A LYS 33 n 33 LYS 33 A TRP 34 n 34 TRP 34 A GLU 35 n 35 GLU 35 A SER 36 n 36 SER 36 A GLY 37 n 37 GLY 37 A TYR 38 n 38 TYR 38 A ASN 39 n 39 ASN 39 A THR 40 n 40 THR 40 A ARG 41 n 41 ARG 41 A ALA 42 n 42 ALA 42 A THR 43 n 43 THR 43 A ASN 44 n 44 ASN 44 A TYR 45 n 45 TYR 45 A ASN 46 n 46 ASN 46 A ALA 47 n 47 ALA 47 A GLY 48 n 48 GLY 48 A ASP 49 n 49 ASP 49 A ARG 50 n 50 ARG 50 A SER 51 n 51 SER 51 A THR 52 n 52 THR 52 A ASP 53 n 53 ASP 53 A TYR 54 n 54 TYR 54 A GLY 55 n 55 GLY 55 A ILE 56 n 56 ILE 56 A PHE 57 n 57 PHE 57 A GLN 58 n 58 GLN 58 A ILE 59 n 59 ILE 59 A ASN 60 n 60 ASN 60 A SER 61 n 61 SER 61 A ARG 62 n 62 ARG 62 A LEU 63 n 63 LEU 63 A TRP 64 n 64 TRP 64 A CYS 65 n 65 CYS 65 A ASN 66 n 66 ASN 66 A ASP 67 n 67 ASP 67 A GLY 68 n 68 GLY 68 A LYS 69 n 69 LYS 69 A THR 70 n 70 THR 70 A PRO 71 n 71 PRO 71 A GLY 72 n 72 GLY 72 A ALA 73 n 73 ALA 73 A VAL 74 n 74 VAL 74 A ASN 75 n 75 ASN 75 A ALA 76 n 76 ALA 76 A CYS 77 n 77 CYS 77 A HIS 78 n 78 HIS 78 A LEU 79 n 79 LEU 79 A SER 80 n 80 SER 80 A CYS 81 n 81 CYS 81 A SER 82 n 82 SER 82 A ALA 83 n 83 ALA 83 A LEU 84 n 84 LEU 84 A LEU 85 n 85 LEU 85 A GLN 86 n 86 GLN 86 A ASP 87 n 87 ASP 87 A ASN 88 n 88 ASN 88 A ILE 89 n 89 ILE 89 A ALA 90 n 90 ALA 90 A ASP 91 n 91 ASP 91 A ALA 92 n 92 ALA 92 A VAL 93 n 93 VAL 93 A ALA 94 n 94 ALA 94 A CYS 95 n 95 CYS 95 A ALA 96 n 96 ALA 96 A LYS 97 n 97 LYS 97 A ARG 98 n 98 ARG 98 A VAL 99 n 99 VAL 99 A VAL 100 n 100 VAL 100 A ARG 101 n 101 ARG 101 A ASP 102 n 102 ASP 102 A PRO 103 n 103 PRO 103 A GLN 104 n 104 GLN 104 A GLY 105 n 105 GLY 105 A ILE 106 n 106 ILE 106 A ARG 107 n 107 ARG 107 A ALA 108 n 108 ALA 108 A TRP 109 n 109 TRP 109 A VAL 110 n 110 VAL 110 A ALA 111 n 111 ALA 111 A TRP 112 n 112 TRP 112 A ARG 113 n 113 ARG 113 A ASN 114 n 114 ASN 114 A ARG 115 n 115 ARG 115 A CYS 116 n 116 CYS 116 A GLN 117 n 117 GLN 117 A ASN 118 n 118 ASN 118 A ARG 119 n 119 ARG 119 A ASP 120 n 120 ASP 120 A VAL 121 n 121 VAL 121 A ARG 122 n 122 ARG 122 A GLN 123 n 123 GLN 123 A TYR 124 n 124 TYR 124 A VAL 125 n 125 VAL 125 A GLN 126 n 126 GLN 126 A GLY 127 n 127 GLY 127 A CYS 128 n 128 CYS 128 A GLY 129 n 129 GLY 129 A VAL 130 n 130 VAL 130 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 N ASN 46 A N ASN 46 A O SER 51 A O SER 51 A O TYR 54 A O TYR 54 A N ILE 59 A N ILE 59 A N ASN 66 A N ASN 66 A O LEU 79 A O LEU 79 1 17.18 2.30 115.30 132.48 A A A CA CB CG LEU LEU LEU 63 63 63 N 1 9.36 1.50 119.30 128.66 A A A C N CA THR PRO PRO 70 71 71 Y 1 A GLN 58 36.14 72.47 98.3 % COMPLETENESS OF DATA 0.216 0.181 0.181 2.23 8.0 3865 RANDOM 1 2 2.23 8.0 43 1101 33 0 1025 0.011 1.87 2.23 22.27 1D6P 52931 40267 0.0 0.1 1 3.4 0.293 2.23 2.32 1 data collection MADNESS data reduction MERGEF (BY K.HARATA) model building X-PLOR refinement X-PLOR 3.1 data reduction MADNESS data scaling MERGEF (K.HARATA) phasing X-PLOR HUMAN LYSOZYME L63 MUTANT LABELLED WITH 2',3'-EPOXYPROPYL N,N'-DIACETYLCHITOBIOSE 1 N N 2 N N 3 N N 4 N N A GLU 4 A GLU 4 HELX_P A LEU 15 A LEU 15 1 1 12 A SER 24 A SER 24 HELX_P A GLY 37 A GLY 37 1 2 14 A SER 82 A SER 82 HELX_P A LEU 85 A LEU 85 5 3 4 A ILE 89 A ILE 89 HELX_P A ASP 102 A ASP 102 1 4 14 A GLN 104 A GLN 104 HELX_P A ALA 108 A ALA 108 5 5 5 A TRP 109 A TRP 109 HELX_P A CYS 116 A CYS 116 1 6 8 A VAL 121 A VAL 121 HELX_P A VAL 125 A VAL 125 5 7 5 disulf 2.034 A CYS 6 A SG CYS 6 1_555 A CYS 128 A SG CYS 128 1_555 disulf 2.023 A CYS 30 A SG CYS 30 1_555 A CYS 116 A SG CYS 116 1_555 disulf 2.027 A CYS 65 A SG CYS 65 1_555 A CYS 81 A SG CYS 81 1_555 disulf 2.023 A CYS 77 A SG CYS 77 1_555 A CYS 95 A SG CYS 95 1_555 covale 1.473 none A ASP 53 A OD1 ASP 53 1_555 A GOL 133 C C3 GOL 1_555 covale 1.363 one A GOL 133 C O1 GOL 1_555 B NAG 1 B C1 NAG 1_555 covale 1.370 both B NAG 1 B O4 NAG 1_555 B NAG 2 B C1 NAG 1_555 HYDROLASE LYSOZYME, MURAMIDASE, HYDROLASE (O-GLYCOSYL), SITE-DIRECTED MUTAGENESIS, N, N'-DIACETYLCHITOBIOSE, AFFINITY LABELING, HYDROLASE LYSC_HUMAN UNP 1 P00695 19 148 1D6P 1 130 P00695 A 1 1 130 1 TYR engineered mutation LEU 63 1D6P A P00695 UNP 81 63 3 2 anti-parallel anti-parallel parallel A THR 43 A THR 43 A ASN 46 A ASN 46 A SER 51 A SER 51 A TYR 54 A TYR 54 A ILE 59 A ILE 59 A ASN 60 A ASN 60 A CYS 65 A CYS 65 A ASN 66 A ASN 66 A LEU 79 A LEU 79 A SER 80 A SER 80 19 P 21 21 21