1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Bewley, C.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 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 C6 H12 O6 180.156 alpha-D-mannopyranose D-saccharide, alpha 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 Structure STRUE6 2005 0969-2126 9 931 940 10.1016/S0969-2126(01)00653-0 11591348 Solution Structure of a Cyanovirin-N:Man alpha 1-2Man alpha Complex. Structural Basis for High Affinity Carbohydrate-Mediated Binding to gp120 2001 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 11022.090 CYANOVIRIN-N 1 nat polymer 342.297 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose 2 man branched 2alpha-alpha-mannobiose no no LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF VSTKINLDDHIANIDGTLKYE LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF VSTKINLDDHIANIDGTLKYE 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 Nostoc sample 45916 Nostoc ellipsosporum atom_site chem_comp entity entity_name_com 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_molecule_features pdbx_nonpoly_scheme pdbx_struct_assembly pdbx_struct_oper_list struct_asym struct_conn struct_site struct_site_gen repository Initial release Carbohydrate remediation repository Remediation Version format compliance Version format compliance Atomic model Data collection Derived calculations Structure summary 1 0 2001-10-24 1 1 2007-10-21 1 2 2011-07-13 2 0 2020-07-29 _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 _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id MAN 201 n B MAN 1 MAN 201 n B MAN 2 MAN 202 n C MAN 1 MAN 202 n C MAN 2 DManpa a-D-mannopyranose a-D-Manp Man RCSB Y RCSB 2001-04-24 REL oligosaccharide DManpa1-2DManpa1-ROH 2 GMML 1.0 Glycam Condensed Sequence WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1 2 PDB2Glycan 1.1.0 WURCS [][a-D-Manp]{[(2+1)][a-D-Manp]{}} 2 PDB-CARE LINUCS C1 O2 MAN MAN 2 1 2 O1 HO2 sing n n RESIDUE NUMBERING: CVN:1-101 MAN:201/202 (CHAIN B) CORRESPONDS TO MAN-ALPHA-1,2-MAN-ALPHA BOUND THROUGH THE HIGH AFFINITY SITE WITH C1-C6 of MAN 201 CORRESPONDING TO THE REDUCING MANNOPYRANOSE RING AND C1-C6 of MAN 202 CORRESPONDING TO C1-C6 OF THE NONREDUCING PYRANOSE. MAN:203/204 (CHAIN C) CORRESPONDS TO MAN-ALPHA-1,2-MAN-ALPHA BOUND THROUGH THE LOW AFFINITY SITE WITH C1-C6 of MAN 203 CORRESPONDING TO THE REDUCING MANNOPYRANOSE RING AND C1-C6 of MAN 204 CORRESPONDING TO C1-C6 OF THE NONREDUCING PYRANOSE. Metabolism oligosaccharide 2alpha-alpha-mannobiose Oligosaccharide This structure is the restrained regularized mean structure. IN THIS ENTRY THE ELEVENTH COLUMN OF THE COORDINATES (with "atom" as the first column) REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE 50 INDIVIDUAL SIMULATED ANNEALING STRUCTURES HAVING ZERO DISTANCE VIOLATIONS GREATER THAN 0.2 A AND ZERO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 5 DEG. THE AVERAGE STRUCTURE WAS GENERATED BY BEST FITTING TO THE BACKBONE OF RESIDUES 1-101. NOTE THE OCCUPANCY FIELD in the tenth column has no meaning. AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND DISACCHARIDE OF THE HIGH AFFINITY SITE=0.36. AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND DISACCHARIDE OF THE LOW AFFINITY SITE=0.58. RMS DEVIATIONS FOR BONDS, ANGLES, IMPROPERS, NOE, CDIH 6.389414E-03 0.717363 0.693234 8.897236E-03 9.181435E-02. 50 1 TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH CBCANH HCCH-COSY HCCH-TOCSY 15N-SEPARATED HOHAHA QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS DIPOLAR COUPLINGS OBTAINED BY TAKING THE DIFFERENCE IN THE J SPLITTINGS IN ISOTROPIC MEDIUM AND IN A LIQUID CRYSTALLINE MEDIUM (5% C12E5, R=0.96) (RUCKERT & OTTING (2000) J.AM.CHEM.SOC. 122, 7793-7797) MEASURED IN 2D IPAP (15N, 1H)-HSQC EXPERIMENTS (OTTIGER ET AL (1998) J.AM.CHEM.SOC. 131, 373-378) INTERMOLECULAR DISTANCE RESTRAINTS OBTAINED FROM 12C-FILTERED/13C-SEPARATED AND 15N-SEPARATED NOE EXPERIMENTS ON COMPLEXES COMPRISING 1:1 AND 1:2 CVN:MAN-ALPHA-(1,2)-MAN-ALPHA INTRA-DISACCHARIDE AND INTER-MANNOPYRANOSE DISTANCE RESTRAINTS OBTAINED FROM 12C-FILTERED NOE AND HOHAHA EXPERIMENTS ON COMPLEXES COMPRISING 1:1 AND 1:2 CVN:MAN-ALPHA-(1,2)-MAN-ALPHA. 6.4 300 K THE STRUCTURE OF THE 1:1 COMPLEX IN WHICH DISACCHARIDE IS BOUND EXCLUSIVELY THROUGH THE HIGH AFFINITY SITE WAS CALCULATED USING CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (BEWLEY AND CLORE (2000) J.AM.CHEM.SOC. 122, 6009-6016; WANG ET AL. (2001) EMBO. J., 19, 5635-5649 & REFS THEREIN) IN WHICH THE PROTEIN BACKBONE AND NON-INTERFACIAL SIDE CHAINS ARE HELD FIXED AND THE DISACCHARIDE AND INTERFACIAL SIDE CHAINS ARE FREE TO TRANSLATE AND ROTATE SUBJECT TO EXPERIMENTAL DISTANCE AND TORSION ANGLE RESTRAINTS. THE STRUCTURE OF THE DISACCHARIDE BOUND THROUGH THE LOW AFFINITY SITE IS A MODEL CALCULATED FROM A COMBINATION OF EXPERIMENTAL DISTANCE AND TORSION ANGLE RESTRAINTS, AND ADDITIONAL RESTRAINTS INTRODUCED ON THE BASIS OF SYMMETRY PRESENT BETWEEN THE TWO DOMAINS (HIGH AND LOW AFFINITY). THE NMR COORDINATES FOR MONOMERIC CVN (PDB ACC. 2EZM) WERE USED FOR THE STARTING COORDINATES WITH 2 EQ. OF MAN-ALPHA-1,2-MAN-ALPHA POSITIONED WITHIN 10 A OF THE PREVIOUSLY MAPPED CARBOHYDRATE BINDING SITES (BEWLEY & OTERO-QUINTERO (2001) J.AM.CHEM.SOC. IN PRESS). CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS BRUNGER refinement X-PLOR NIH 500 Bruker DMX500 600 Bruker DMX600 LEU 1 n 1 LEU 1 A GLY 2 n 2 GLY 2 A LYS 3 n 3 LYS 3 A PHE 4 n 4 PHE 4 A SER 5 n 5 SER 5 A GLN 6 n 6 GLN 6 A THR 7 n 7 THR 7 A CYS 8 n 8 CYS 8 A TYR 9 n 9 TYR 9 A ASN 10 n 10 ASN 10 A SER 11 n 11 SER 11 A ALA 12 n 12 ALA 12 A ILE 13 n 13 ILE 13 A GLN 14 n 14 GLN 14 A GLY 15 n 15 GLY 15 A SER 16 n 16 SER 16 A VAL 17 n 17 VAL 17 A LEU 18 n 18 LEU 18 A THR 19 n 19 THR 19 A SER 20 n 20 SER 20 A THR 21 n 21 THR 21 A CYS 22 n 22 CYS 22 A GLU 23 n 23 GLU 23 A ARG 24 n 24 ARG 24 A THR 25 n 25 THR 25 A ASN 26 n 26 ASN 26 A GLY 27 n 27 GLY 27 A GLY 28 n 28 GLY 28 A TYR 29 n 29 TYR 29 A ASN 30 n 30 ASN 30 A THR 31 n 31 THR 31 A SER 32 n 32 SER 32 A SER 33 n 33 SER 33 A ILE 34 n 34 ILE 34 A ASP 35 n 35 ASP 35 A LEU 36 n 36 LEU 36 A ASN 37 n 37 ASN 37 A SER 38 n 38 SER 38 A VAL 39 n 39 VAL 39 A ILE 40 n 40 ILE 40 A GLU 41 n 41 GLU 41 A ASN 42 n 42 ASN 42 A VAL 43 n 43 VAL 43 A ASP 44 n 44 ASP 44 A GLY 45 n 45 GLY 45 A SER 46 n 46 SER 46 A LEU 47 n 47 LEU 47 A LYS 48 n 48 LYS 48 A TRP 49 n 49 TRP 49 A GLN 50 n 50 GLN 50 A PRO 51 n 51 PRO 51 A SER 52 n 52 SER 52 A ASN 53 n 53 ASN 53 A PHE 54 n 54 PHE 54 A ILE 55 n 55 ILE 55 A GLU 56 n 56 GLU 56 A THR 57 n 57 THR 57 A CYS 58 n 58 CYS 58 A ARG 59 n 59 ARG 59 A ASN 60 n 60 ASN 60 A THR 61 n 61 THR 61 A GLN 62 n 62 GLN 62 A LEU 63 n 63 LEU 63 A ALA 64 n 64 ALA 64 A GLY 65 n 65 GLY 65 A SER 66 n 66 SER 66 A SER 67 n 67 SER 67 A GLU 68 n 68 GLU 68 A LEU 69 n 69 LEU 69 A ALA 70 n 70 ALA 70 A ALA 71 n 71 ALA 71 A GLU 72 n 72 GLU 72 A CYS 73 n 73 CYS 73 A LYS 74 n 74 LYS 74 A THR 75 n 75 THR 75 A ARG 76 n 76 ARG 76 A ALA 77 n 77 ALA 77 A GLN 78 n 78 GLN 78 A GLN 79 n 79 GLN 79 A PHE 80 n 80 PHE 80 A VAL 81 n 81 VAL 81 A SER 82 n 82 SER 82 A THR 83 n 83 THR 83 A LYS 84 n 84 LYS 84 A ILE 85 n 85 ILE 85 A ASN 86 n 86 ASN 86 A LEU 87 n 87 LEU 87 A ASP 88 n 88 ASP 88 A ASP 89 n 89 ASP 89 A HIS 90 n 90 HIS 90 A ILE 91 n 91 ILE 91 A ALA 92 n 92 ALA 92 A ASN 93 n 93 ASN 93 A ILE 94 n 94 ILE 94 A ASP 95 n 95 ASP 95 A GLY 96 n 96 GLY 96 A THR 97 n 97 THR 97 A LEU 98 n 98 LEU 98 A LYS 99 n 99 LYS 99 A TYR 100 n 100 TYR 100 A GLU 101 n 101 GLU 101 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 GLN 14 A O GLN 14 A N VAL 17 A N VAL 17 A O CYS 22 A O CYS 22 A N ASN 30 A N ASN 30 A N VAL 43 A N VAL 43 A O SER 46 A O SER 46 A N ALA 64 A N ALA 64 A O GLU 68 A O GLU 68 A O CYS 73 A O CYS 73 A N VAL 81 A N VAL 81 A N ILE 94 A N ILE 94 A O THR 97 A O THR 97 1 A SER 52 174.41 12.36 CYANOVIRIN-N Solution NMR Structure of Complex of 1:2 Cyanovirin-N:Man-Alpha1,2-Man-Alpha Restrained Regularized Mean Coordinates 1 N N 2 N N 2 N N A LYS 3 A LYS 3 HELX_P A GLN 6 A GLN 6 5 1 4 A ASN 53 A ASN 53 HELX_P A GLU 56 A GLU 56 5 2 4 disulf 2.023 A CYS 8 A SG CYS 8 1_555 A CYS 22 A SG CYS 22 1_555 disulf 2.019 A CYS 58 A SG CYS 58 1_555 A CYS 73 A SG CYS 73 1_555 covale 1.443 both B MAN 1 B O2 MAN 1_555 B MAN 2 B C1 MAN 1_555 covale 1.442 both C MAN 1 C O2 MAN 1_555 C MAN 2 C C1 MAN 1_555 ANTIVIRAL PROTEIN HIV-INACTIVATING PROTEIN, MAN-ALPHA1, 2-MAN-ALPHA, ANTIVIRAL PROTEIN CVN_NOSEL UNP 1 1 P81180 LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF VSTKINLDDHIANIDGTLKYE 1 101 1IIY 1 101 P81180 A 1 1 101 3 2 3 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A CYS 8 A CYS 8 A GLN 14 A GLN 14 A VAL 17 A VAL 17 A GLU 23 A GLU 23 A TYR 29 A TYR 29 A ASP 35 A ASP 35 A ILE 40 A ILE 40 A VAL 43 A VAL 43 A SER 46 A SER 46 A TRP 49 A TRP 49 A CYS 58 A CYS 58 A ALA 64 A ALA 64 A GLU 68 A GLU 68 A LYS 74 A LYS 74 A PHE 80 A PHE 80 A ASN 86 A ASN 86 A ILE 91 A ILE 91 A ILE 94 A ILE 94 A THR 97 A THR 97 A TYR 100 A TYR 100