HEADER IMMUNE SYSTEM 23-DEC-23 8XKJ TITLE CKAPPA DOMAIN OF HUMAN IMMUNOGLOBULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN KAPPA LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CKAPPA DOMAIN; COMPND 5 SYNONYM: IMMUNOGLOBULIN KAPPA LIGHT CHAIN EU; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURE FROM CYANA 3.98.15, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.YANAKA,A.KODAMA,Y.MIYANOIRI,K.KATO REVDAT 1 05-FEB-25 8XKJ 0 JRNL AUTH S.YANAKA,A.KODAMA,S.NISHIGUCHI,R.FUJITA,J.SHEN,P.BOONSRI, JRNL AUTH 2 D.SUNG,Y.ISONO,H.YAGI,Y.MIYANOIRI,T.UCHIHASHI,K.KATO JRNL TITL IDENTIFICATION OF POTENTIAL C1-BINDING SITES IN THE JRNL TITL 2 IMMUNOGLOBULIN CL DOMAINS. JRNL REF INT.IMMUNOL. V. 36 405 2024 JRNL REFN ESSN 1460-2377 JRNL PMID 38564192 JRNL DOI 10.1093/INTIMM/DXAE017 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARTINA REMARK 3 AUTHORS : KLUKOWSKI, P., RIEK, R. AND GUNTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8XKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300043667. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : NOT DEFINED REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-13C; U-15N] PROTEIN, 5 REMARK 210 MM NAPI, 50 MM SODIUM CHLORIDE, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 3D 1H-13C NOESY; REMARK 210 3D C(CO)NH; 3D CBCA(CO)NH; 3D REMARK 210 CBCANH; 3D HBHA(CO)NH; 3D HNCA; REMARK 210 3D HNCO; 3D HN(CO)CA; 3D HNCACO; REMARK 210 3D CCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANACE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, ARTINA REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 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 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 PRO A 5 -169.65 -69.77 REMARK 500 1 ASN A 30 111.65 -39.91 REMARK 500 1 GLU A 35 32.02 -93.57 REMARK 500 1 ASN A 50 34.96 -96.54 REMARK 500 1 ASP A 59 -178.53 -57.53 REMARK 500 1 LYS A 82 -30.11 -160.72 REMARK 500 1 HIS A 90 -176.42 -179.92 REMARK 500 1 GLU A 107 44.62 -98.46 REMARK 500 2 PRO A 5 -169.27 -69.72 REMARK 500 2 GLU A 35 32.04 -93.18 REMARK 500 2 ASN A 50 35.25 -96.42 REMARK 500 2 ASP A 59 -178.65 -57.68 REMARK 500 2 LYS A 82 -30.93 -162.21 REMARK 500 2 HIS A 90 -178.14 -178.76 REMARK 500 2 ASN A 108 35.87 -158.82 REMARK 500 3 PRO A 5 -166.83 -69.75 REMARK 500 3 TYR A 32 -74.97 -89.38 REMARK 500 3 GLU A 35 46.92 -83.99 REMARK 500 3 ASN A 50 34.73 -96.77 REMARK 500 3 ASP A 59 179.81 -55.70 REMARK 500 3 LYS A 82 -30.48 -160.41 REMARK 500 3 HIS A 90 -174.04 -170.68 REMARK 500 3 SER A 106 175.63 -57.46 REMARK 500 3 GLU A 107 49.30 -89.57 REMARK 500 3 ASN A 108 36.32 -147.91 REMARK 500 3 PHE A 111 -73.08 -52.12 REMARK 500 4 PRO A 5 -170.16 -69.80 REMARK 500 4 GLU A 35 34.18 -91.76 REMARK 500 4 ASN A 50 34.62 -97.21 REMARK 500 4 GLN A 52 119.62 -165.19 REMARK 500 4 ASP A 59 178.81 -59.11 REMARK 500 4 LYS A 82 -30.59 -160.28 REMARK 500 4 GLU A 107 43.72 -92.31 REMARK 500 5 PRO A 5 -170.32 -69.71 REMARK 500 5 ASN A 30 111.65 -39.64 REMARK 500 5 GLU A 35 38.44 -91.42 REMARK 500 5 ASN A 50 33.99 -96.98 REMARK 500 5 GLN A 52 119.37 -167.93 REMARK 500 5 ASP A 59 -177.50 -57.95 REMARK 500 5 LYS A 82 -30.04 -161.61 REMARK 500 5 HIS A 90 -176.16 -179.34 REMARK 500 5 TYR A 110 103.29 -51.88 REMARK 500 6 PRO A 5 -171.49 -69.79 REMARK 500 6 ASN A 30 108.74 -39.83 REMARK 500 6 GLU A 35 42.52 -92.96 REMARK 500 6 ASN A 50 34.25 -97.01 REMARK 500 6 GLN A 52 119.07 -167.23 REMARK 500 6 ASP A 59 -178.38 -57.61 REMARK 500 6 LYS A 82 -31.01 -161.42 REMARK 500 6 HIS A 90 -178.37 -173.68 REMARK 500 REMARK 500 THIS ENTRY HAS 173 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36630 RELATED DB: BMRB REMARK 900 CKAPPA DOMAIN OF HUMAN IMMUNOGLOBULIN DBREF 8XKJ A 2 105 UNP P0DOX7 IGK_HUMAN 110 213 SEQADV 8XKJ SER A 106 UNP P0DOX7 EXPRESSION TAG SEQADV 8XKJ GLU A 107 UNP P0DOX7 EXPRESSION TAG SEQADV 8XKJ ASN A 108 UNP P0DOX7 EXPRESSION TAG SEQADV 8XKJ LEU A 109 UNP P0DOX7 EXPRESSION TAG SEQADV 8XKJ TYR A 110 UNP P0DOX7 EXPRESSION TAG SEQADV 8XKJ PHE A 111 UNP P0DOX7 EXPRESSION TAG SEQADV 8XKJ GLN A 112 UNP P0DOX7 EXPRESSION TAG SEQRES 1 A 111 VAL ALA ALA PRO SER VAL PHE ILE PHE PRO PRO SER ASP SEQRES 2 A 111 GLU GLN LEU LYS SER GLY THR ALA SER VAL VAL CYS LEU SEQRES 3 A 111 LEU ASN ASN PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP SEQRES 4 A 111 LYS VAL ASP ASN ALA LEU GLN SER GLY ASN SER GLN GLU SEQRES 5 A 111 SER VAL THR GLU GLN ASP SER LYS ASP SER THR TYR SER SEQRES 6 A 111 LEU SER SER THR LEU THR LEU SER LYS ALA ASP TYR GLU SEQRES 7 A 111 LYS HIS LYS VAL TYR ALA CYS GLU VAL THR HIS GLN GLY SEQRES 8 A 111 LEU SER SER PRO VAL THR LYS SER PHE ASN ARG GLY GLU SEQRES 9 A 111 SER GLU ASN LEU TYR PHE GLN HELIX 1 AA1 SER A 13 SER A 19 1 7 HELIX 2 AA2 LYS A 75 LYS A 80 1 6 SHEET 1 AA1 3 VAL A 7 PHE A 10 0 SHEET 2 AA1 3 VAL A 25 LEU A 28 -1 O LEU A 27 N PHE A 8 SHEET 3 AA1 3 LEU A 67 THR A 70 -1 O LEU A 67 N LEU A 28 SHEET 1 AA2 2 THR A 21 ALA A 22 0 SHEET 2 AA2 2 LEU A 73 SER A 74 -1 O LEU A 73 N ALA A 22 SHEET 1 AA3 4 ALA A 45 LEU A 46 0 SHEET 2 AA3 4 LYS A 37 VAL A 42 -1 N VAL A 42 O ALA A 45 SHEET 3 AA3 4 VAL A 83 THR A 89 -1 O GLU A 87 N GLN A 39 SHEET 4 AA3 4 SER A 100 ASN A 102 -1 O PHE A 101 N TYR A 84 LINK SG CYS A 26 SG CYS A 86 1555 1555 1.76 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 TER 1694 GLN A 112 ENDMDL MODEL 2 TER 1694 GLN A 112 ENDMDL MODEL 3 TER 1694 GLN A 112 ENDMDL MODEL 4 TER 1694 GLN A 112 ENDMDL MODEL 5 TER 1694 GLN A 112 ENDMDL MODEL 6 TER 1694 GLN A 112 ENDMDL MODEL 7 TER 1694 GLN A 112 ENDMDL MODEL 8 TER 1694 GLN A 112 ENDMDL MODEL 9 TER 1694 GLN A 112 ENDMDL MODEL 10 TER 1694 GLN A 112 ENDMDL MODEL 11 TER 1694 GLN A 112 ENDMDL MODEL 12 TER 1694 GLN A 112 ENDMDL MODEL 13 TER 1694 GLN A 112 ENDMDL MODEL 14 TER 1694 GLN A 112 ENDMDL MODEL 15 TER 1694 GLN A 112 ENDMDL MODEL 16 TER 1694 GLN A 112 ENDMDL MODEL 17 TER 1694 GLN A 112 ENDMDL MODEL 18 TER 1694 GLN A 112 ENDMDL MODEL 19 TER 1694 GLN A 112 ENDMDL MODEL 20 TER 1694 GLN A 112 ENDMDL CONECT 351 1288 CONECT 1288 351 MASTER 146 0 0 2 9 0 0 6 865 1 2 9 END