HEADER NEUROPEPTIDE 16-JUL-20 6ZSS TITLE NMR STRUCTURE OF WATER-SOLUBLE DOMAIN OF HUMAN LYNX2 (LYPD1) PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LY6/PLAUR DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE HELA TUMOR SUPPRESSOR,PHTS; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LYPD1, LYPDC1, PSEC0181, UNQ3079/PRO9917; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SHUFFLE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-22B(+) KEYWDS LY-6, LY6/UPAR, THREE-FINGER PROTEIN, NICOTINIC ACETYLCHOLINE KEYWDS 2 RECEPTOR, LYNX, LYNX2, LYPD1, SNAKE NEUROTOXIN, NEUROPEPTIDE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.V.KOCHAROVSKAYA,A.S.PARAMONOV,E.N.LYUKMANOVA,Z.O.SHENKAREV REVDAT 2 14-JUN-23 6ZSS 1 REMARK REVDAT 1 13-JAN-21 6ZSS 0 JRNL AUTH A.S.PARAMONOV,M.V.KOCHAROVSKAYA,A.V.TSAREV,D.S.KULBATSKII, JRNL AUTH 2 E.V.LOKTYUSHOV,M.A.SHULEPKO,M.P.KIRPICHNIKOV,E.N.LYUKMANOVA, JRNL AUTH 3 Z.O.SHENKAREV JRNL TITL STRUCTURAL DIVERSITY AND DYNAMICS OF HUMAN THREE-FINGER JRNL TITL 2 PROTEINS ACTING ON NICOTINIC ACETYLCHOLINE RECEPTORS. JRNL REF INT J MOL SCI V. 21 2020 JRNL REFN ESSN 1422-0067 JRNL PMID 33019770 JRNL DOI 10.3390/IJMS21197280 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.13 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZSS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292108951. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 0.25 MM [U-98% 13C; U-98% 15N] REMARK 210 LYNX2, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCACO; 3D HN(CO)CA; REMARK 210 3D HNCACB; 2D 1H-13C HSQC; 2D 1H- REMARK 210 15N HSQC; 3D 1H-15N-NOESY-HSQC; REMARK 210 3D 1H-15N-TOCSY-HSQC; 3D 1H-13C- REMARK 210 HCCH-TOCSY; 3D HNHA; 3D HNHB; 2D REMARK 210 1H-13C TROSY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CARA 1.8, MDDNMR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LEU A 111 51.60 -100.36 REMARK 500 1 SER A 116 47.29 -150.91 REMARK 500 1 ASP A 130 28.28 -144.68 REMARK 500 1 SER A 148 166.62 178.24 REMARK 500 1 TYR A 162 179.41 -56.59 REMARK 500 1 ASN A 172 44.45 -91.98 REMARK 500 2 GLU A 108 80.57 -151.06 REMARK 500 2 ASN A 112 83.36 64.92 REMARK 500 2 ASP A 114 33.60 -99.32 REMARK 500 2 SER A 116 33.38 -93.41 REMARK 500 2 ASP A 130 22.96 -156.73 REMARK 500 2 SER A 148 164.23 178.37 REMARK 500 2 SER A 159 -75.00 -52.63 REMARK 500 2 CYS A 166 -171.09 -175.32 REMARK 500 3 CYS A 106 81.80 -152.91 REMARK 500 3 GLN A 110 148.42 -179.78 REMARK 500 3 LEU A 111 -67.90 -100.49 REMARK 500 3 SER A 148 162.31 178.52 REMARK 500 3 SER A 159 -75.67 -77.11 REMARK 500 3 SER A 164 45.68 -92.90 REMARK 500 4 GLN A 110 -177.26 -176.95 REMARK 500 4 ASP A 114 93.83 -168.33 REMARK 500 4 SER A 148 165.76 179.05 REMARK 500 4 ASN A 172 54.22 -115.30 REMARK 500 5 PHE A 109 178.54 -55.90 REMARK 500 5 GLN A 110 141.19 179.77 REMARK 500 5 THR A 125 174.30 -57.00 REMARK 500 5 ASP A 130 -40.86 -166.09 REMARK 500 5 SER A 148 160.51 179.08 REMARK 500 5 TYR A 162 -179.06 -66.46 REMARK 500 5 CYS A 166 116.90 -163.09 REMARK 500 5 ASN A 172 43.09 -91.37 REMARK 500 6 CYS A 106 86.16 -151.79 REMARK 500 6 LEU A 111 -73.60 -100.55 REMARK 500 6 ASP A 114 111.06 -166.47 REMARK 500 6 ASN A 127 151.02 179.94 REMARK 500 6 ASP A 130 77.49 -166.98 REMARK 500 6 SER A 148 161.69 178.12 REMARK 500 6 GLN A 163 58.52 -96.15 REMARK 500 6 SER A 164 36.13 -146.45 REMARK 500 6 ASN A 172 44.84 -92.94 REMARK 500 7 GLU A 108 84.23 -151.07 REMARK 500 7 CYS A 115 44.47 -93.59 REMARK 500 7 ASN A 123 77.11 -106.21 REMARK 500 7 VAL A 128 -175.81 -60.63 REMARK 500 7 SER A 151 -168.18 -121.63 REMARK 500 7 ASN A 172 45.02 -104.76 REMARK 500 8 GLN A 110 144.65 178.92 REMARK 500 8 LEU A 111 -65.05 -100.84 REMARK 500 8 ASP A 114 99.33 -162.36 REMARK 500 REMARK 500 THIS ENTRY HAS 154 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34532 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF WATER-SOLUBLE DOMAIN OF HUMAN LYNX2 (LYPD1) PROTEIN DBREF 6ZSS A 101 185 UNP Q8N2G4 LYPD1_HUMAN 23 107 SEQADV 6ZSS MET A 100 UNP Q8N2G4 INITIATING METHIONINE SEQRES 1 A 86 MET ILE GLN CYS TYR GLN CYS GLU GLU PHE GLN LEU ASN SEQRES 2 A 86 ASN ASP CYS SER SER PRO GLU PHE ILE VAL ASN CYS THR SEQRES 3 A 86 VAL ASN VAL GLN ASP MET CYS GLN LYS GLU VAL MET GLU SEQRES 4 A 86 GLN SER ALA GLY ILE MET TYR ARG LYS SER CYS ALA SER SEQRES 5 A 86 SER ALA ALA CYS LEU ILE ALA SER ALA GLY TYR GLN SER SEQRES 6 A 86 PHE CYS SER PRO GLY LYS LEU ASN SER VAL CYS ILE SER SEQRES 7 A 86 CYS CYS ASN THR PRO LEU CYS ASN HELIX 1 AA1 SER A 152 GLY A 161 1 10 SHEET 1 AA1 2 CYS A 103 TYR A 104 0 SHEET 2 AA1 2 ILE A 121 VAL A 122 -1 O VAL A 122 N CYS A 103 SHEET 1 AA2 3 ILE A 143 SER A 151 0 SHEET 2 AA2 3 GLN A 129 GLU A 138 -1 N MET A 137 O MET A 144 SHEET 3 AA2 3 CYS A 175 CYS A 179 -1 O SER A 177 N LYS A 134 SSBOND 1 CYS A 103 CYS A 132 1555 1555 1.96 SSBOND 2 CYS A 106 CYS A 115 1555 1555 1.96 SSBOND 3 CYS A 124 CYS A 149 1555 1555 1.97 SSBOND 4 CYS A 155 CYS A 178 1555 1555 1.88 SSBOND 5 CYS A 166 CYS A 175 1555 1555 1.99 SSBOND 6 CYS A 179 CYS A 184 1555 1555 1.94 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1