PDB Short entry for 1L3H HEADER IMMUNE SYSTEM 27-FEB-02 1L3H TITLE NMR STRUCTURE OF P41ICF, A POTENT INHIBITOR OF HUMAN CATHEPSIN L COMPND MOL_ID: 1; COMPND 2 MOLECULE: MHC CLASS II-ASSOCIATED P41 INVARIANT CHAIN FRAGMENT COMPND 3 (P41ICF); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: THYROGLOBULIN-LIKE DOMAIN; COMPND 6 SYNONYM: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, GAMMA CHAIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. KEYWDS ALPHA HELIX, BETA SHEET, DISULFIDE BONDS, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR C.CHIVA,P.BARTHE,A.CODINA,E.GIRALT REVDAT 3 23-FEB-22 1L3H 1 REMARK REVDAT 2 24-FEB-09 1L3H 1 VERSN REVDAT 1 04-MAR-03 1L3H 0 JRNL AUTH C.CHIVA,P.BARTHE,A.CODINA,M.GAIRI,F.MOLINA,C.GRANIER, JRNL AUTH 2 M.PUGNIERE,T.INUI,H.NISHIO,Y.NISHIUCHI,T.KIMURA, JRNL AUTH 3 S.SAKAKIBARA,F.ALBERICIO,E.GIRALT JRNL TITL SYNTHESIS AND NMR STRUCTURE OF P41ICF, A POTENT INHIBITOR OF JRNL TITL 2 HUMAN CATHEPSIN L JRNL REF J.AM.CHEM.SOC. V. 125 1508 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 12568610 JRNL DOI 10.1021/JA0207908 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, AMBER 5.0 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 981 RESTRAINTS, 925 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 56 REMARK 3 DIHEDRAL ANGLE RESTRAINTS REMARK 4 REMARK 4 1L3H COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015607. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 5.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM P41ICF; 20MM PHOSPHATE REMARK 210 BUFFER, 0.01MM NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D TOCSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND REMARK 210 SIMULATED ANNEALING WITH REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY,TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HG1 THR A 2 O GLY A 27 1.49 REMARK 500 O GLN A 5 HG SER A 9 1.54 REMARK 500 O SER A 18 HG SER A 37 1.56 REMARK 500 OD1 ASN A 47 HG1 THR A 49 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 TYR A 35 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 12 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 14 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 17 TYR A 35 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 19 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 22 TYR A 35 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 22 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 24 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 25 TYR A 40 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 14 47.62 -73.92 REMARK 500 1 PRO A 31 -8.53 -51.25 REMARK 500 1 ARG A 55 103.81 -51.69 REMARK 500 1 SER A 63 33.17 -65.81 REMARK 500 1 GLU A 64 4.08 -61.64 REMARK 500 2 PRO A 52 18.82 -69.15 REMARK 500 2 ARG A 55 94.27 -56.77 REMARK 500 2 ARG A 57 1.13 -63.56 REMARK 500 2 SER A 63 62.99 -167.58 REMARK 500 3 PRO A 52 23.20 -70.15 REMARK 500 3 ARG A 55 102.84 -45.54 REMARK 500 3 ASN A 61 49.55 -76.29 REMARK 500 3 CYS A 62 107.87 -56.10 REMARK 500 3 GLU A 64 23.69 -69.63 REMARK 500 4 LYS A 3 -62.14 -21.62 REMARK 500 4 HIS A 15 61.79 -116.40 REMARK 500 4 ASN A 53 -5.02 65.11 REMARK 500 4 ARG A 55 91.89 -60.95 REMARK 500 4 ASN A 61 61.68 -112.11 REMARK 500 4 CYS A 62 106.66 -52.24 REMARK 500 4 SER A 63 25.39 47.22 REMARK 500 5 ARG A 55 106.08 -59.89 REMARK 500 5 ARG A 57 1.50 -65.50 REMARK 500 6 PRO A 31 -9.09 -54.45 REMARK 500 6 ASN A 53 6.63 59.73 REMARK 500 6 ARG A 55 109.21 -42.42 REMARK 500 6 GLU A 64 68.90 -62.63 REMARK 500 7 PRO A 31 -18.76 -48.21 REMARK 500 7 ASN A 53 -0.47 61.22 REMARK 500 7 ARG A 55 95.22 -43.57 REMARK 500 7 SER A 63 18.30 -64.96 REMARK 500 8 HIS A 15 70.87 -111.03 REMARK 500 8 ASN A 53 -0.82 65.18 REMARK 500 8 ARG A 55 98.82 -56.44 REMARK 500 8 CYS A 62 -172.64 -65.32 REMARK 500 8 SER A 63 51.63 -64.70 REMARK 500 8 GLU A 64 32.84 -69.65 REMARK 500 9 HIS A 15 63.68 -111.41 REMARK 500 9 ASN A 53 -2.55 59.44 REMARK 500 9 ARG A 55 99.02 -46.16 REMARK 500 9 ARG A 57 23.33 -79.27 REMARK 500 9 GLU A 64 26.10 -75.34 REMARK 500 10 HIS A 15 53.62 -114.86 REMARK 500 10 GLU A 25 0.15 -64.64 REMARK 500 10 ARG A 55 94.17 -62.83 REMARK 500 10 CYS A 62 105.73 -57.16 REMARK 500 10 SER A 63 19.31 54.29 REMARK 500 11 ARG A 55 103.02 -43.80 REMARK 500 11 ARG A 57 13.72 -69.07 REMARK 500 12 HIS A 15 63.19 -114.36 REMARK 500 REMARK 500 THIS ENTRY HAS 129 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 14 TYR A 35 0.07 SIDE CHAIN REMARK 500 18 ARG A 20 0.08 SIDE CHAIN REMARK 500 23 TYR A 35 0.11 SIDE CHAIN REMARK 500 27 TYR A 29 0.08 SIDE CHAIN REMARK 500 29 ARG A 55 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ICF RELATED DB: PDB REMARK 900 1ICF CONTAINS THE SAME PROTEIN COMPLEXED WITH CATHEPSIN L. DBREF 1L3H A 1 65 UNP P04233 HG2A_HUMAN 210 274 SEQRES 1 A 65 LEU THR LYS CYS GLN GLU GLU VAL SER HIS ILE PRO ALA SEQRES 2 A 65 VAL HIS PRO GLY SER PHE ARG PRO LYS CYS ASP GLU ASN SEQRES 3 A 65 GLY ASN TYR LEU PRO LEU GLN CYS TYR GLY SER ILE GLY SEQRES 4 A 65 TYR CYS TRP CYS VAL PHE PRO ASN GLY THR GLU VAL PRO SEQRES 5 A 65 ASN THR ARG SER ARG GLY HIS HIS ASN CYS SER GLU SER HELIX 1 1 THR A 2 ILE A 11 1 10 SHEET 1 A 2 LEU A 32 TYR A 35 0 SHEET 2 A 2 TYR A 40 CYS A 43 -1 O TRP A 42 N GLN A 33 SSBOND 1 CYS A 4 CYS A 23 1555 1555 2.03 SSBOND 2 CYS A 34 CYS A 41 1555 1555 2.05 SSBOND 3 CYS A 43 CYS A 62 1555 1555 2.03 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