HEADER LIPID TRANSPORT 17-APR-09 3H3T TITLE CRYSTAL STRUCTURE OF THE CERT START DOMAIN IN COMPLEX WITH HPA-16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOODPASTURE ANTIGEN BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CERT START DOMAIN (RESIDUES 347-598); COMPND 5 SYNONYM: CDNA FLJ77923, HIGHLY SIMILAR TO HOMO SAPIENS COLLAGEN, TYPE COMPND 6 IV, ALPHA 3 (GOODPASTURE ANTIGEN) BINDING PROTEIN, COL4A3BP, COMPND 7 TRANSCRIPT VARIANT 2, MRNA, COLLAGEN, TYPE IV, ALPHA 3 (GOODPASTURE COMPND 8 ANTIGEN) BINDING PROTEIN, ISOFORM CRA_A; COMPND 9 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; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-5X1 (MODIFIED) KEYWDS LIPID TRANSFER PROTEIN, CERT, CERAMIDE TRANSFER, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR N.KUDO,S.WAKATSUKI,R.KATO REVDAT 3 01-NOV-23 3H3T 1 REMARK SEQADV REVDAT 2 01-NOV-17 3H3T 1 REMARK REVDAT 1 02-MAR-10 3H3T 0 JRNL AUTH N.KUDO,K.KUMAGAI,R.MATSUBARA,S.KOBAYASHI,K.HANADA, JRNL AUTH 2 S.WAKATSUKI,R.KATO JRNL TITL CRYSTAL STRUCTURES OF THE CERT START DOMAIN WITH INHIBITORS JRNL TITL 2 PROVIDE INSIGHTS INTO THE MECHANISM OF CERAMIDE TRANSFER. JRNL REF J.MOL.BIOL. V. 396 245 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20036255 JRNL DOI 10.1016/J.JMB.2009.12.029 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18577 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 948 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1269 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3776 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.34000 REMARK 3 B22 (A**2) : 0.31000 REMARK 3 B33 (A**2) : 0.69000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.50000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.675 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.302 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.304 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3926 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5334 ; 1.469 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 468 ; 6.476 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 191 ;33.818 ;24.346 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 649 ;16.320 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;21.106 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 593 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2986 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2351 ; 0.718 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3840 ; 1.381 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1575 ; 1.957 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1494 ; 3.342 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3H3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18692 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0820 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2E3N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, TEMPERATURE 293K, REMARK 280 VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 37.28400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THERE ARE 2 BIOLOGICAL UNITS IN THE ASYMMETRIC UNIT. 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 344 REMARK 465 ASN A 345 REMARK 465 SER A 346 REMARK 465 LEU A 347 REMARK 465 HIS A 348 REMARK 465 TRP A 349 REMARK 465 PRO A 350 REMARK 465 THR A 351 REMARK 465 SER A 352 REMARK 465 LEU A 353 REMARK 465 PRO A 354 REMARK 465 SER A 355 REMARK 465 GLY A 356 REMARK 465 ASP A 357 REMARK 465 ALA A 358 REMARK 465 PHE A 359 REMARK 465 SER A 360 REMARK 465 SER A 361 REMARK 465 VAL A 362 REMARK 465 SER B 344 REMARK 465 ASN B 345 REMARK 465 SER B 346 REMARK 465 LEU B 347 REMARK 465 HIS B 348 REMARK 465 TRP B 349 REMARK 465 PRO B 350 REMARK 465 THR B 351 REMARK 465 SER B 352 REMARK 465 LEU B 353 REMARK 465 PRO B 354 REMARK 465 SER B 355 REMARK 465 GLY B 356 REMARK 465 ASP B 357 REMARK 465 ALA B 358 REMARK 465 PHE B 359 REMARK 465 SER B 360 REMARK 465 SER B 361 REMARK 465 VAL B 362 REMARK 465 GLY B 363 REMARK 465 THR B 364 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL B 368 CB CG1 CG2 REMARK 470 GLU B 537 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OG1 THR B 493 OD2 ASP B 496 2.06 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 THR A 364 77.24 -110.34 REMARK 500 ASP A 416 101.74 -13.13 REMARK 500 ALA A 512 78.22 -157.20 REMARK 500 ASN A 516 -54.02 -26.20 REMARK 500 GLU B 398 106.79 -165.79 REMARK 500 ASP B 416 99.16 -15.71 REMARK 500 ALA B 475 -179.47 -173.99 REMARK 500 HIS B 509 132.50 -172.18 REMARK 500 LEU B 514 156.71 -47.13 REMARK 500 PRO B 535 151.33 -28.80 REMARK 500 ARG B 544 7.15 -67.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 16H A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 16H B 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2E3M RELATED DB: PDB REMARK 900 THE SAME PROTEIN, IN THE APO-FORM REMARK 900 RELATED ID: 2E3N RELATED DB: PDB REMARK 900 THE SAME PROTEIN, COMPLEXED WITH C6-CERAMIDE REMARK 900 RELATED ID: 2E3O RELATED DB: PDB REMARK 900 THE SAME PROTEIN, COMPLEXED WITH C16-CERAMIDE REMARK 900 RELATED ID: 2E3P RELATED DB: PDB REMARK 900 THE SAME PROTEIN, COMPLEXED WITH C16-CERAMIDE REMARK 900 RELATED ID: 2E3Q RELATED DB: PDB REMARK 900 THE SAME PROTEIN, COMPLEXED WITH C18-CERAMIDE REMARK 900 RELATED ID: 2E3R RELATED DB: PDB REMARK 900 THE SAME PROTEIN, COMPLEXED WITH C18-CERAMIDE REMARK 900 RELATED ID: 2E3S RELATED DB: PDB REMARK 900 THE SAME PROTEIN, CO-CRYSTALLIZED WITH C24-CERAMIDE REMARK 900 RELATED ID: 3H3Q RELATED DB: PDB REMARK 900 RELATED ID: 3H3R RELATED DB: PDB REMARK 900 RELATED ID: 3H3S RELATED DB: PDB DBREF 3H3T A 347 598 UNP A8K7S2 A8K7S2_HUMAN 347 598 DBREF 3H3T B 347 598 UNP A8K7S2 A8K7S2_HUMAN 347 598 SEQADV 3H3T SER A 344 UNP A8K7S2 EXPRESSION TAG SEQADV 3H3T ASN A 345 UNP A8K7S2 EXPRESSION TAG SEQADV 3H3T SER A 346 UNP A8K7S2 EXPRESSION TAG SEQADV 3H3T SER B 344 UNP A8K7S2 EXPRESSION TAG SEQADV 3H3T ASN B 345 UNP A8K7S2 EXPRESSION TAG SEQADV 3H3T SER B 346 UNP A8K7S2 EXPRESSION TAG SEQRES 1 A 255 SER ASN SER LEU HIS TRP PRO THR SER LEU PRO SER GLY SEQRES 2 A 255 ASP ALA PHE SER SER VAL GLY THR HIS ARG PHE VAL GLN SEQRES 3 A 255 LYS VAL GLU GLU MET VAL GLN ASN HIS MET THR TYR SER SEQRES 4 A 255 LEU GLN ASP VAL GLY GLY ASP ALA ASN TRP GLN LEU VAL SEQRES 5 A 255 VAL GLU GLU GLY GLU MET LYS VAL TYR ARG ARG GLU VAL SEQRES 6 A 255 GLU GLU ASN GLY ILE VAL LEU ASP PRO LEU LYS ALA THR SEQRES 7 A 255 HIS ALA VAL LYS GLY VAL THR GLY HIS GLU VAL CYS ASN SEQRES 8 A 255 TYR PHE TRP ASN VAL ASP VAL ARG ASN ASP TRP GLU THR SEQRES 9 A 255 THR ILE GLU ASN PHE HIS VAL VAL GLU THR LEU ALA ASP SEQRES 10 A 255 ASN ALA ILE ILE ILE TYR GLN THR HIS LYS ARG VAL TRP SEQRES 11 A 255 PRO ALA SER GLN ARG ASP VAL LEU TYR LEU SER VAL ILE SEQRES 12 A 255 ARG LYS ILE PRO ALA LEU THR GLU ASN ASP PRO GLU THR SEQRES 13 A 255 TRP ILE VAL CYS ASN PHE SER VAL ASP HIS ASP SER ALA SEQRES 14 A 255 PRO LEU ASN ASN ARG CYS VAL ARG ALA LYS ILE ASN VAL SEQRES 15 A 255 ALA MET ILE CYS GLN THR LEU VAL SER PRO PRO GLU GLY SEQRES 16 A 255 ASN GLN GLU ILE SER ARG ASP ASN ILE LEU CYS LYS ILE SEQRES 17 A 255 THR TYR VAL ALA ASN VAL ASN PRO GLY GLY TRP ALA PRO SEQRES 18 A 255 ALA SER VAL LEU ARG ALA VAL ALA LYS ARG GLU TYR PRO SEQRES 19 A 255 LYS PHE LEU LYS ARG PHE THR SER TYR VAL GLN GLU LYS SEQRES 20 A 255 THR ALA GLY LYS PRO ILE LEU PHE SEQRES 1 B 255 SER ASN SER LEU HIS TRP PRO THR SER LEU PRO SER GLY SEQRES 2 B 255 ASP ALA PHE SER SER VAL GLY THR HIS ARG PHE VAL GLN SEQRES 3 B 255 LYS VAL GLU GLU MET VAL GLN ASN HIS MET THR TYR SER SEQRES 4 B 255 LEU GLN ASP VAL GLY GLY ASP ALA ASN TRP GLN LEU VAL SEQRES 5 B 255 VAL GLU GLU GLY GLU MET LYS VAL TYR ARG ARG GLU VAL SEQRES 6 B 255 GLU GLU ASN GLY ILE VAL LEU ASP PRO LEU LYS ALA THR SEQRES 7 B 255 HIS ALA VAL LYS GLY VAL THR GLY HIS GLU VAL CYS ASN SEQRES 8 B 255 TYR PHE TRP ASN VAL ASP VAL ARG ASN ASP TRP GLU THR SEQRES 9 B 255 THR ILE GLU ASN PHE HIS VAL VAL GLU THR LEU ALA ASP SEQRES 10 B 255 ASN ALA ILE ILE ILE TYR GLN THR HIS LYS ARG VAL TRP SEQRES 11 B 255 PRO ALA SER GLN ARG ASP VAL LEU TYR LEU SER VAL ILE SEQRES 12 B 255 ARG LYS ILE PRO ALA LEU THR GLU ASN ASP PRO GLU THR SEQRES 13 B 255 TRP ILE VAL CYS ASN PHE SER VAL ASP HIS ASP SER ALA SEQRES 14 B 255 PRO LEU ASN ASN ARG CYS VAL ARG ALA LYS ILE ASN VAL SEQRES 15 B 255 ALA MET ILE CYS GLN THR LEU VAL SER PRO PRO GLU GLY SEQRES 16 B 255 ASN GLN GLU ILE SER ARG ASP ASN ILE LEU CYS LYS ILE SEQRES 17 B 255 THR TYR VAL ALA ASN VAL ASN PRO GLY GLY TRP ALA PRO SEQRES 18 B 255 ALA SER VAL LEU ARG ALA VAL ALA LYS ARG GLU TYR PRO SEQRES 19 B 255 LYS PHE LEU LYS ARG PHE THR SER TYR VAL GLN GLU LYS SEQRES 20 B 255 THR ALA GLY LYS PRO ILE LEU PHE HET 16H A 600 30 HET 16H B 600 30 HETNAM 16H N-[(1R,3R)-3-HYDROXY-1-(HYDROXYMETHYL)-3- HETNAM 2 16H PHENYLPROPYL]HEXADECANAMIDE FORMUL 3 16H 2(C26 H45 N O3) FORMUL 5 HOH *35(H2 O) HELIX 1 1 PHE A 367 SER A 382 1 16 HELIX 2 2 THR A 428 ASN A 438 1 11 HELIX 3 3 VAL A 441 GLU A 446 1 6 HELIX 4 4 SER A 543 ASP A 545 5 3 HELIX 5 5 PRO A 564 ALA A 592 1 29 HELIX 6 6 PHE B 367 SER B 382 1 16 HELIX 7 7 THR B 428 ASN B 438 1 11 HELIX 8 8 VAL B 441 GLU B 446 1 6 HELIX 9 9 PRO B 564 ALA B 592 1 29 SHEET 1 A 9 GLN A 393 GLU A 398 0 SHEET 2 A 9 MET A 401 ARG A 405 -1 O VAL A 403 N VAL A 396 SHEET 3 A 9 LEU A 418 LYS A 425 -1 O LYS A 419 N TYR A 404 SHEET 4 A 9 ILE A 547 ASN A 558 -1 O TYR A 553 N ALA A 420 SHEET 5 A 9 LYS A 522 VAL A 533 -1 N ILE A 528 O THR A 552 SHEET 6 A 9 THR A 499 SER A 506 -1 N ASN A 504 O VAL A 525 SHEET 7 A 9 ARG A 478 ILE A 489 -1 N ILE A 489 O THR A 499 SHEET 8 A 9 ALA A 462 HIS A 469 -1 N ILE A 465 O TYR A 482 SHEET 9 A 9 ILE A 449 ALA A 459 -1 N GLU A 450 O THR A 468 SHEET 1 B 8 GLN A 393 GLU A 398 0 SHEET 2 B 8 MET A 401 ARG A 405 -1 O VAL A 403 N VAL A 396 SHEET 3 B 8 LEU A 418 LYS A 425 -1 O LYS A 419 N TYR A 404 SHEET 4 B 8 ILE A 547 ASN A 558 -1 O TYR A 553 N ALA A 420 SHEET 5 B 8 LYS A 522 VAL A 533 -1 N ILE A 528 O THR A 552 SHEET 6 B 8 THR A 499 SER A 506 -1 N ASN A 504 O VAL A 525 SHEET 7 B 8 ARG A 478 ILE A 489 -1 N ILE A 489 O THR A 499 SHEET 8 B 8 VAL A 519 ARG A 520 1 O VAL A 519 N ASP A 479 SHEET 1 C 2 GLU A 409 GLU A 410 0 SHEET 2 C 2 ILE A 413 VAL A 414 -1 O ILE A 413 N GLU A 410 SHEET 1 D 9 GLN B 393 GLU B 398 0 SHEET 2 D 9 MET B 401 ARG B 405 -1 O VAL B 403 N VAL B 396 SHEET 3 D 9 LEU B 418 LYS B 425 -1 O LYS B 419 N TYR B 404 SHEET 4 D 9 ILE B 547 ASN B 558 -1 O ILE B 551 N HIS B 422 SHEET 5 D 9 LYS B 522 VAL B 533 -1 N ILE B 528 O THR B 552 SHEET 6 D 9 THR B 499 SER B 506 -1 N ASN B 504 O VAL B 525 SHEET 7 D 9 ARG B 478 ILE B 489 -1 N ILE B 489 O THR B 499 SHEET 8 D 9 ALA B 462 HIS B 469 -1 N ILE B 463 O SER B 484 SHEET 9 D 9 ILE B 449 ALA B 459 -1 N ASN B 451 O THR B 468 SHEET 1 E 8 GLN B 393 GLU B 398 0 SHEET 2 E 8 MET B 401 ARG B 405 -1 O VAL B 403 N VAL B 396 SHEET 3 E 8 LEU B 418 LYS B 425 -1 O LYS B 419 N TYR B 404 SHEET 4 E 8 ILE B 547 ASN B 558 -1 O ILE B 551 N HIS B 422 SHEET 5 E 8 LYS B 522 VAL B 533 -1 N ILE B 528 O THR B 552 SHEET 6 E 8 THR B 499 SER B 506 -1 N ASN B 504 O VAL B 525 SHEET 7 E 8 ARG B 478 ILE B 489 -1 N ILE B 489 O THR B 499 SHEET 8 E 8 VAL B 519 ARG B 520 1 O VAL B 519 N ASP B 479 SHEET 1 F 2 GLU B 409 GLU B 410 0 SHEET 2 F 2 ILE B 413 VAL B 414 -1 O ILE B 413 N GLU B 410 SITE 1 AC1 15 PHE A 436 ARG A 442 GLU A 446 ILE A 449 SITE 2 AC1 15 GLN A 467 VAL A 472 TRP A 473 TYR A 482 SITE 3 AC1 15 ASN A 504 ALA A 521 VAL A 525 TYR A 553 SITE 4 AC1 15 VAL A 557 TYR A 576 PHE A 579 SITE 1 AC2 11 PHE B 436 ARG B 442 GLU B 446 GLN B 467 SITE 2 AC2 11 HIS B 469 TYR B 482 ASN B 504 ILE B 523 SITE 3 AC2 11 VAL B 525 TYR B 553 TYR B 576 CRYST1 42.340 74.568 78.021 90.00 102.84 90.00 P 1 21 1 4 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 0.023618 0.000000 0.005382 0.00000 SCALE2 0.000000 0.013411 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013146 0.00000 TER 1900 PHE A 598 TER 3780 PHE B 598 HETATM 3781 O21 16H A 600 8.316 0.921 33.637 1.00 30.52 O HETATM 3782 C21 16H A 600 7.889 1.480 32.640 1.00 29.61 C HETATM 3783 N2 16H A 600 7.067 0.955 31.719 1.00 26.74 N HETATM 3784 C2 16H A 600 6.347 -0.310 31.809 1.00 28.81 C HETATM 3785 C1 16H A 600 4.981 -0.256 31.118 1.00 29.93 C HETATM 3786 O1 16H A 600 5.061 0.263 29.776 1.00 29.92 O HETATM 3787 C3 16H A 600 7.226 -1.448 31.272 1.00 29.66 C HETATM 3788 C4 16H A 600 8.442 -1.195 32.159 1.00 30.99 C HETATM 3789 C5 16H A 600 9.730 -0.945 31.466 1.00 31.17 C HETATM 3790 C6 16H A 600 9.866 -1.122 30.103 1.00 31.50 C HETATM 3791 C7 16H A 600 11.094 -0.790 29.534 1.00 32.70 C HETATM 3792 C8 16H A 600 12.147 -0.267 30.280 1.00 31.16 C HETATM 3793 C9 16H A 600 11.987 -0.065 31.637 1.00 29.07 C HETATM 3794 C10 16H A 600 10.772 -0.388 32.203 1.00 30.13 C HETATM 3795 O4 16H A 600 8.462 -1.910 33.393 1.00 31.72 O HETATM 3796 C22 16H A 600 8.298 2.913 32.434 1.00 32.96 C HETATM 3797 C23 16H A 600 9.615 3.012 31.687 1.00 33.79 C HETATM 3798 C24 16H A 600 9.838 4.470 31.325 1.00 35.77 C HETATM 3799 C25 16H A 600 11.321 4.747 31.155 1.00 39.95 C HETATM 3800 C26 16H A 600 11.783 4.131 29.845 1.00 42.09 C HETATM 3801 C27 16H A 600 13.265 3.825 29.880 1.00 45.44 C HETATM 3802 C28 16H A 600 13.872 4.148 28.518 1.00 48.71 C HETATM 3803 C29 16H A 600 15.231 3.469 28.319 1.00 52.51 C HETATM 3804 C30 16H A 600 15.214 2.617 27.053 1.00 55.30 C HETATM 3805 C31 16H A 600 13.780 2.172 26.713 1.00 56.26 C HETATM 3806 C32 16H A 600 13.690 1.340 25.437 1.00 55.98 C HETATM 3807 C33 16H A 600 14.913 0.447 25.296 1.00 55.96 C HETATM 3808 C34 16H A 600 14.971 -0.562 26.432 1.00 55.95 C HETATM 3809 C35 16H A 600 13.810 -1.526 26.263 1.00 56.32 C HETATM 3810 C36 16H A 600 13.489 -2.184 27.580 1.00 57.03 C HETATM 3811 O21 16H B 600 -4.121 0.768 -3.990 1.00 27.05 O HETATM 3812 C21 16H B 600 -4.491 1.334 -5.017 1.00 26.28 C HETATM 3813 N2 16H B 600 -5.422 0.820 -5.849 1.00 22.04 N HETATM 3814 C2 16H B 600 -6.243 -0.355 -5.543 1.00 22.71 C HETATM 3815 C1 16H B 600 -7.557 -0.295 -6.324 1.00 22.87 C HETATM 3816 O1 16H B 600 -7.289 0.160 -7.664 1.00 21.19 O HETATM 3817 C3 16H B 600 -5.493 -1.657 -5.883 1.00 22.90 C HETATM 3818 C4 16H B 600 -4.145 -1.443 -5.176 1.00 23.34 C HETATM 3819 C5 16H B 600 -2.911 -1.368 -6.037 1.00 22.37 C HETATM 3820 C6 16H B 600 -2.940 -1.656 -7.396 1.00 20.94 C HETATM 3821 C7 16H B 600 -1.774 -1.482 -8.147 1.00 20.97 C HETATM 3822 C8 16H B 600 -0.591 -0.997 -7.585 1.00 19.93 C HETATM 3823 C9 16H B 600 -0.569 -0.680 -6.232 1.00 20.31 C HETATM 3824 C10 16H B 600 -1.727 -0.862 -5.478 1.00 21.76 C HETATM 3825 O4 16H B 600 -4.062 -2.115 -3.929 1.00 23.08 O HETATM 3826 C22 16H B 600 -3.891 2.702 -5.337 1.00 25.88 C HETATM 3827 C23 16H B 600 -3.052 2.683 -6.611 1.00 27.62 C HETATM 3828 C24 16H B 600 -2.046 3.831 -6.675 1.00 29.44 C HETATM 3829 C25 16H B 600 -1.340 3.890 -8.039 1.00 32.14 C HETATM 3830 C26 16H B 600 -0.275 2.813 -8.261 1.00 31.40 C HETATM 3831 C27 16H B 600 1.149 3.363 -8.146 1.00 34.89 C HETATM 3832 C28 16H B 600 2.136 2.943 -9.276 1.00 35.64 C HETATM 3833 C29 16H B 600 3.537 2.536 -8.742 1.00 35.50 C HETATM 3834 C30 16H B 600 4.463 1.698 -9.650 1.00 33.13 C HETATM 3835 C31 16H B 600 4.053 0.226 -9.802 1.00 31.06 C HETATM 3836 C32 16H B 600 3.518 0.010 -11.216 1.00 32.98 C HETATM 3837 C33 16H B 600 2.541 -1.156 -11.391 1.00 32.90 C HETATM 3838 C34 16H B 600 1.110 -0.695 -11.639 1.00 33.30 C HETATM 3839 C35 16H B 600 1.008 0.766 -12.055 1.00 35.90 C HETATM 3840 C36 16H B 600 -0.238 1.412 -11.459 1.00 36.26 C HETATM 3841 O HOH A 2 9.463 2.957 49.426 1.00 26.27 O HETATM 3842 O HOH A 6 12.414 -9.337 18.850 1.00 35.57 O HETATM 3843 O HOH A 8 15.859 18.904 46.020 1.00 44.78 O HETATM 3844 O HOH A 10 8.797 16.234 44.265 1.00 33.96 O HETATM 3845 O HOH A 12 18.539 -0.586 33.969 1.00 16.50 O HETATM 3846 O HOH A 14 17.743 0.948 32.353 1.00 18.42 O HETATM 3847 O HOH A 15 11.566 -9.516 27.118 1.00 29.00 O HETATM 3848 O HOH A 16 10.878 6.545 48.888 1.00 38.13 O HETATM 3849 O HOH A 20 1.169 -3.464 33.608 1.00 23.22 O HETATM 3850 O HOH A 21 -0.932 1.732 33.517 1.00 30.00 O HETATM 3851 O HOH A 22 4.663 -21.151 39.175 1.00 42.34 O HETATM 3852 O HOH A 23 3.897 5.934 24.205 1.00 39.73 O HETATM 3853 O HOH A 25 -9.362 14.155 50.233 1.00 30.79 O HETATM 3854 O HOH A 28 -0.763 0.835 54.708 1.00 25.09 O HETATM 3855 O HOH A 29 -2.154 -9.305 46.497 1.00 39.89 O HETATM 3856 O HOH A 31 19.700 -7.165 33.041 1.00 29.93 O HETATM 3857 O HOH A 35 -0.596 -21.530 33.391 1.00 26.48 O HETATM 3858 O HOH B 3 5.434 0.344 -5.411 1.00 20.02 O HETATM 3859 O HOH B 4 -21.476 15.434 11.852 1.00 32.26 O HETATM 3860 O HOH B 5 -3.973 -16.344 -12.542 1.00 32.92 O HETATM 3861 O HOH B 7 5.069 17.446 -2.111 1.00 22.16 O HETATM 3862 O HOH B 9 -2.007 -12.458 -9.678 1.00 35.37 O HETATM 3863 O HOH B 11 16.331 8.277 5.039 1.00 19.69 O HETATM 3864 O HOH B 13 5.851 6.126 10.147 1.00 32.17 O HETATM 3865 O HOH B 17 -1.621 -9.904 -9.629 1.00 24.72 O HETATM 3866 O HOH B 18 -11.515 -3.817 -3.147 1.00 22.88 O HETATM 3867 O HOH B 19 -13.253 1.904 -4.290 1.00 23.73 O HETATM 3868 O HOH B 24 6.216 -1.094 -3.743 1.00 19.87 O HETATM 3869 O HOH B 26 7.578 -0.249 -8.123 1.00 33.05 O HETATM 3870 O HOH B 27 -2.685 3.954 11.476 1.00 33.70 O HETATM 3871 O HOH B 30 9.732 16.491 9.798 1.00 25.89 O HETATM 3872 O HOH B 32 -9.379 7.505 20.814 1.00 32.17 O HETATM 3873 O HOH B 33 16.701 0.917 11.470 1.00 37.17 O HETATM 3874 O HOH B 34 -7.018 -21.063 3.650 1.00 20.46 O HETATM 3875 O HOH B 36 7.601 1.519 -4.386 1.00 23.91 O CONECT 3781 3782 CONECT 3782 3781 3783 3796 CONECT 3783 3782 3784 CONECT 3784 3783 3785 3787 CONECT 3785 3784 3786 CONECT 3786 3785 CONECT 3787 3784 3788 CONECT 3788 3787 3789 3795 CONECT 3789 3788 3790 3794 CONECT 3790 3789 3791 CONECT 3791 3790 3792 CONECT 3792 3791 3793 CONECT 3793 3792 3794 CONECT 3794 3789 3793 CONECT 3795 3788 CONECT 3796 3782 3797 CONECT 3797 3796 3798 CONECT 3798 3797 3799 CONECT 3799 3798 3800 CONECT 3800 3799 3801 CONECT 3801 3800 3802 CONECT 3802 3801 3803 CONECT 3803 3802 3804 CONECT 3804 3803 3805 CONECT 3805 3804 3806 CONECT 3806 3805 3807 CONECT 3807 3806 3808 CONECT 3808 3807 3809 CONECT 3809 3808 3810 CONECT 3810 3809 CONECT 3811 3812 CONECT 3812 3811 3813 3826 CONECT 3813 3812 3814 CONECT 3814 3813 3815 3817 CONECT 3815 3814 3816 CONECT 3816 3815 CONECT 3817 3814 3818 CONECT 3818 3817 3819 3825 CONECT 3819 3818 3820 3824 CONECT 3820 3819 3821 CONECT 3821 3820 3822 CONECT 3822 3821 3823 CONECT 3823 3822 3824 CONECT 3824 3819 3823 CONECT 3825 3818 CONECT 3826 3812 3827 CONECT 3827 3826 3828 CONECT 3828 3827 3829 CONECT 3829 3828 3830 CONECT 3830 3829 3831 CONECT 3831 3830 3832 CONECT 3832 3831 3833 CONECT 3833 3832 3834 CONECT 3834 3833 3835 CONECT 3835 3834 3836 CONECT 3836 3835 3837 CONECT 3837 3836 3838 CONECT 3838 3837 3839 CONECT 3839 3838 3840 CONECT 3840 3839 MASTER 358 0 2 9 38 0 7 6 3871 2 60 40 END