0.022777 0.000000 0.000000 0.000000 0.016822 0.000000 0.000000 0.000000 0.010140 0.00000 0.00000 0.00000 Lee, S.-C. Guan, H.-H. Wang, C.-H. Huang, W.-N. Chen, C.-J. Wu, W.-G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 43.903 59.447 98.620 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 C6 H8 O7 192.124 CITRIC ACID non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer C6 H10 O10 S 274.203 n 2-O-sulfo-alpha-L-idopyranuronic acid O2-SULFO-GLUCURONIC ACID L-saccharide, alpha 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 C6 H13 N O11 S2 339.298 n 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose D-saccharide, alpha linking C4 H9 N O3 119.119 y THREONINE 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 J.Biol.Chem. JBCHA3 0071 0021-9258 280 9567 9577 10.1074/jbc.M412398200 15590643 Structural basis of citrate-dependent and heparan sulfate-mediated cell surface retention of cobra cardiotoxin A3 2005 IDS C 6 HAS WRONG CHIRALITY AT ATOM C5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 110 1 IMAGE PLATE 2004-07-15 MARRESEARCH Si 111 CHANNEL SINGLE WAVELENGTH M x-ray 1 1.1274 1.0 BL17B2 NSRRC 1.1274 SYNCHROTRON NSRRC BEAMLINE BL17B2 6758.330 Cytotoxin 3 2 nat polymer 1750.427 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose 1 man branched 192.124 CITRIC ACID 1 syn non-polymer 18.015 water 10 nat water Cardiotoxin 3, CTX-3, Cardiotoxin analog III, CTX III no no LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 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 Chinese cobra Naja sample 8656 Naja atra 1 1.893 35.07 VAPOR DIFFUSION, HANGING DROP 5.6 PEG4000, isopropanol, trisodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K 291 software atom_site chem_comp database_PDB_caveat 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 pdbx_unobs_or_zero_occ_atoms pdbx_validate_chiral struct_asym struct_conn struct_site struct_site_gen repository Initial release Carbohydrate remediation repository Remediation Version format compliance Non-polymer description Version format compliance Refinement description Advisory Atomic model Data collection Derived calculations Structure summary 1 0 2004-12-14 1 1 2008-04-30 1 2 2011-07-13 1 3 2017-10-11 2 0 2020-07-29 _software.classification _software.name _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_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _pdbx_struct_assembly_gen.asym_id_list _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_seq_id _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.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 _struct_conn.ptnr2_label_seq_id A SGN 66 n C SGN 1 A IDS 65 n C IDS 2 A SGN 64 n C SGN 3 A IDS 63 n C IDS 4 A SGN 62 n C SGN 5 A IDS 61 n C IDS 6 a-L-IdopA2SO3 DGlcpNS[6S]a N-sulfo-6-sulfo-a-D-glucopyranose a-D-GlcpNSO36SO3 RCSB Y PDBJ 2004-10-21 REL oligosaccharide WURCS=2.0/2,6,5/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1 2 PDB2Glycan 1.1.0 WURCS [][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}} 2 PDB-CARE LINUCS C1 O4 IDS SGN 2 1 2 O1 HO4 sing C1 O4 SGN IDS 3 2 2 O1 HO4 sing C1 O4 IDS SGN 4 3 2 O1 HO4 sing C1 O4 SGN IDS 5 4 2 O1 HO4 sing C1 O4 IDS SGN 6 5 2 O1 HO4 sing n n n n n n CIT CITRIC ACID HOH water CIT 101 3 CIT CIT 101 A HOH 102 4 HOH HOH 102 A HOH 103 4 HOH HOH 103 A HOH 104 4 HOH HOH 104 A HOH 105 4 HOH HOH 105 A HOH 106 4 HOH HOH 106 A HOH 107 4 HOH HOH 107 A HOH 108 4 HOH HOH 108 A HOH 109 4 HOH HOH 109 A HOH 110 4 HOH HOH 110 A HOH 61 4 HOH HOH 61 B LEU 1 n 1 LEU 1 A LYS 2 n 2 LYS 2 A CYS 3 n 3 CYS 3 A ASN 4 n 4 ASN 4 A LYS 5 n 5 LYS 5 A LEU 6 n 6 LEU 6 A VAL 7 n 7 VAL 7 A PRO 8 n 8 PRO 8 A LEU 9 n 9 LEU 9 A PHE 10 n 10 PHE 10 A TYR 11 n 11 TYR 11 A LYS 12 n 12 LYS 12 A THR 13 n 13 THR 13 A CYS 14 n 14 CYS 14 A PRO 15 n 15 PRO 15 A ALA 16 n 16 ALA 16 A GLY 17 n 17 GLY 17 A LYS 18 n 18 LYS 18 A ASN 19 n 19 ASN 19 A LEU 20 n 20 LEU 20 A CYS 21 n 21 CYS 21 A TYR 22 n 22 TYR 22 A LYS 23 n 23 LYS 23 A MET 24 n 24 MET 24 A PHE 25 n 25 PHE 25 A MET 26 n 26 MET 26 A VAL 27 n 27 VAL 27 A ALA 28 n 28 ALA 28 A THR 29 n 29 THR 29 A PRO 30 n 30 PRO 30 A LYS 31 n 31 LYS 31 A VAL 32 n 32 VAL 32 A PRO 33 n 33 PRO 33 A VAL 34 n 34 VAL 34 A LYS 35 n 35 LYS 35 A ARG 36 n 36 ARG 36 A GLY 37 n 37 GLY 37 A CYS 38 n 38 CYS 38 A ILE 39 n 39 ILE 39 A ASP 40 n 40 ASP 40 A VAL 41 n 41 VAL 41 A CYS 42 n 42 CYS 42 A PRO 43 n 43 PRO 43 A LYS 44 n 44 LYS 44 A SER 45 n 45 SER 45 A SER 46 n 46 SER 46 A LEU 47 n 47 LEU 47 A LEU 48 n 48 LEU 48 A VAL 49 n 49 VAL 49 A LYS 50 n 50 LYS 50 A TYR 51 n 51 TYR 51 A VAL 52 n 52 VAL 52 A CYS 53 n 53 CYS 53 A CYS 54 n 54 CYS 54 A ASN 55 n 55 ASN 55 A THR 56 n 56 THR 56 A ASP 57 n 57 ASP 57 A ARG 58 n 58 ARG 58 A CYS 59 n 59 CYS 59 A ASN 60 n 60 ASN 60 A LEU 1 n 1 LEU 1 B LYS 2 n 2 LYS 2 B CYS 3 n 3 CYS 3 B ASN 4 n 4 ASN 4 B LYS 5 n 5 LYS 5 B LEU 6 n 6 LEU 6 B VAL 7 n 7 VAL 7 B PRO 8 n 8 PRO 8 B LEU 9 n 9 LEU 9 B PHE 10 n 10 PHE 10 B TYR 11 n 11 TYR 11 B LYS 12 n 12 LYS 12 B THR 13 n 13 THR 13 B CYS 14 n 14 CYS 14 B PRO 15 n 15 PRO 15 B ALA 16 n 16 ALA 16 B GLY 17 n 17 GLY 17 B LYS 18 n 18 LYS 18 B ASN 19 n 19 ASN 19 B LEU 20 n 20 LEU 20 B CYS 21 n 21 CYS 21 B TYR 22 n 22 TYR 22 B LYS 23 n 23 LYS 23 B MET 24 n 24 MET 24 B PHE 25 n 25 PHE 25 B MET 26 n 26 MET 26 B VAL 27 n 27 VAL 27 B ALA 28 n 28 ALA 28 B THR 29 n 29 THR 29 B PRO 30 n 30 PRO 30 B LYS 31 n 31 LYS 31 B VAL 32 n 32 VAL 32 B PRO 33 n 33 PRO 33 B VAL 34 n 34 VAL 34 B LYS 35 n 35 LYS 35 B ARG 36 n 36 ARG 36 B GLY 37 n 37 GLY 37 B CYS 38 n 38 CYS 38 B ILE 39 n 39 ILE 39 B ASP 40 n 40 ASP 40 B VAL 41 n 41 VAL 41 B CYS 42 n 42 CYS 42 B PRO 43 n 43 PRO 43 B LYS 44 n 44 LYS 44 B SER 45 n 45 SER 45 B SER 46 n 46 SER 46 B LEU 47 n 47 LEU 47 B LEU 48 n 48 LEU 48 B VAL 49 n 49 VAL 49 B LYS 50 n 50 LYS 50 B TYR 51 n 51 TYR 51 B VAL 52 n 52 VAL 52 B CYS 53 n 53 CYS 53 B CYS 54 n 54 CYS 54 B ASN 55 n 55 ASN 55 B THR 56 n 56 THR 56 B ASP 57 n 57 ASP 57 B ARG 58 n 58 ARG 58 B CYS 59 n 59 CYS 59 B ASN 60 n 60 ASN 60 B author_and_software_defined_assembly PISA 2 dimeric 2780 -1 8100 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_555 -x+1/2,y+1/2,-z+1/2 crystal symmetry operation 21.9515000000 29.7235000000 49.3100000000 A N CYS 3 A N CYS 3 A O LYS 12 A O LYS 12 A O GLY 37 A O GLY 37 A N TYR 22 A N TYR 22 A N LYS 23 A N LYS 23 A O VAL 52 A O VAL 52 B O LYS 35 B O LYS 35 B N MET 24 B N MET 24 B N CYS 21 B N CYS 21 B O CYS 54 B O CYS 54 1 C O4 IDS 6 C O4 IDS 6 1 N 1 C C5 IDS 6 PLANAR 1 A A O2 O2 CIT CIT 101 101 2.19 1_555 3_555 1 A LEU 9 -60.89 2.30 1 A ALA 16 -31.28 135.49 1 A LYS 18 -52.28 92.70 1 A ASN 19 -105.25 49.61 1 A SER 46 -93.65 -134.16 1 A LEU 47 -98.26 -62.58 1 B THR 13 -50.01 103.49 1 B PRO 15 -59.33 -179.01 1 B VAL 27 -20.26 -43.15 1 B THR 29 -150.31 73.82 1 B VAL 32 -102.68 64.26 1 B ASP 40 -61.42 -90.97 1 B SER 45 -80.87 -159.55 1 B SER 46 -148.17 -157.71 0.25 0.227 0.242 0.231 2.4 25 245 5051 4889 RANDOM 1 0 MOLECULAR REPLACEMENT Engh & Huber 2.4 25 10 1058 118 0 930 0.005 1.170 2.4 25 1XT3 5051 4889 0 0 0.038 1 4.1 96.8 2.4 2.48 1 83.6 data scaling XDS data scaling SCALEPACK refinement CNS data reduction XDS phasing CNS Cytotoxin 3 Structure Basis of Venom Citrate-Dependent Heparin Sulfate-Mediated Cell Surface Retention of Cobra Cardiotoxin A3 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N disulf 2.027 A CYS 3 A SG CYS 3 1_555 A CYS 21 A SG CYS 21 1_555 disulf 2.029 A CYS 14 A SG CYS 14 1_555 A CYS 38 A SG CYS 38 1_555 disulf 2.029 A CYS 42 A SG CYS 42 1_555 A CYS 53 A SG CYS 53 1_555 disulf 2.023 A CYS 54 A SG CYS 54 1_555 A CYS 59 A SG CYS 59 1_555 disulf 2.030 B CYS 3 B SG CYS 3 1_555 B CYS 14 B SG CYS 14 1_555 disulf 2.027 B CYS 3 B SG CYS 3 1_555 B CYS 21 B SG CYS 21 1_555 disulf 2.026 B CYS 14 B SG CYS 14 1_555 B CYS 38 B SG CYS 38 1_555 disulf 2.031 B CYS 42 B SG CYS 42 1_555 B CYS 53 B SG CYS 53 1_555 disulf 2.029 B CYS 54 B SG CYS 54 1_555 B CYS 59 B SG CYS 59 1_555 covale 1.420 both C SGN 1 C O4 SGN 1_555 C IDS 2 C C1 IDS 1_555 covale 1.428 both C IDS 2 C O4 IDS 1_555 C SGN 3 C C1 SGN 1_555 covale 1.461 both C SGN 3 C O4 SGN 1_555 C IDS 4 C C1 IDS 1_555 covale 1.433 both C IDS 4 C O4 IDS 1_555 C SGN 5 C C1 SGN 1_555 covale 1.442 both C SGN 5 C O4 SGN 1_555 C IDS 6 C C1 IDS 1_555 TOXIN CTX-3, heparin, citrate, Toxin CTX3_NAJAT UNP 1 22 P60301 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 22 81 1XT3 1 60 P60301 A 1 1 60 22 81 1XT3 1 60 P60301 B 1 1 60 2 3 3 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A LYS 2 A LYS 2 A ASN 4 A ASN 4 A TYR 11 A TYR 11 A THR 13 A THR 13 A LYS 35 A LYS 35 A CYS 38 A CYS 38 A CYS 21 A CYS 21 A MET 26 A MET 26 A VAL 49 A VAL 49 A CYS 54 A CYS 54 B LYS 35 B LYS 35 B CYS 38 B CYS 38 B CYS 21 B CYS 21 B MET 26 B MET 26 B VAL 49 B VAL 49 B CYS 54 B CYS 54 20 C 2 2 21