HEADER OXYGEN TRANSPORT 08-JUL-16 5KSI TITLE CRYSTAL STRUCTURE OF DEOXYGENATED HEMOGLOBIN IN COMPLEX WITH TITLE 2 SPHINGOSINE PHOSPHATE AND 2,3-BISPHOSPHOGLYCERATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN SUBUNIT ALPHA; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: ALPHA-GLOBIN,HEMOGLOBIN ALPHA CHAIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEMOGLOBIN SUBUNIT BETA; COMPND 7 CHAIN: B, D; COMPND 8 SYNONYM: BETA-GLOBIN,HEMOGLOBIN BETA CHAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606 KEYWDS HEMOGLOBIN, SPHINGOSINE-1-PHOSPHATE, COMPLEX, ALLOSTERIC EFFECTOR, KEYWDS 2 OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.H.AHMED,M.K.SAFO,Y.XIA REVDAT 4 04-OCT-23 5KSI 1 REMARK REVDAT 3 04-DEC-19 5KSI 1 REMARK REVDAT 2 06-DEC-17 5KSI 1 JRNL REVDAT 1 26-JUL-17 5KSI 0 JRNL AUTH K.SUN,A.D'ALESSANDRO,M.H.AHMED,Y.ZHANG,A.SONG,T.P.KO, JRNL AUTH 2 T.NEMKOV,J.A.REISZ,H.WU,M.ADEBIYI,Z.PENG,J.GONG,H.LIU, JRNL AUTH 3 A.HUANG,Y.E.WEN,A.Q.WEN,V.BERKA,M.V.BOGDANOV,O.ABDULMALIK, JRNL AUTH 4 L.HAN,A.L.TSAI,M.IDOWU,H.S.JUNEJA,R.E.KELLEMS,W.DOWHAN, JRNL AUTH 5 K.C.HANSEN,M.K.SAFO,Y.XIA JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHT OF SPHINGOSINE JRNL TITL 2 1-PHOSPHATE-MEDIATED PATHOGENIC METABOLIC REPROGRAMMING IN JRNL TITL 3 SICKLE CELL DISEASE. JRNL REF SCI REP V. 7 15281 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 29127281 JRNL DOI 10.1038/S41598-017-13667-8 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 54123 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2764 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4384 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 286 REMARK 3 SOLVENT ATOMS : 784 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.66700 REMARK 3 B22 (A**2) : -4.46500 REMARK 3 B33 (A**2) : 2.79800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.199 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.602 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.987 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.760 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 89.89 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 AUTHOR PROVIDED THE FOLLOWING EVIDENCE OF DIRECT S1P BINDING TO REMARK 3 HEMOGLOBIN: S1P BEADS SUCCESSFULLY PULLED DOWN HBA FROM NORMAL REMARK 3 HUMAN ERYTHROCYTE LYSATES, WHILE SPHINGOSINE OR LYSOPHOSPHATIDIC REMARK 3 ACID BEADS FAILED TO PULL DOWN HB. REMARK 3 IN ADDITION, CO-BINDING OF 2,3-DPG AND S1P TO HEMOGLOBIN (HB) IS REMARK 3 REQUIRED FOR S1P-INDUCED DECREASE IN HB-O2 AFFINITY. WE MEASURED REMARK 3 OXYGEN EQUILIBRATION CURVES (OEC) OF PURIFIED HBA IN THE PRESENCE REMARK 3 OF 2,3-DPG ALONG WITH S1P. WE FOUND THAT S1P DECREASED HBA-O2 REMARK 3 BINDING AFFINITY WITH INCREASED P50 IN A DOSE-DEPENDENT MANNER. REMARK 3 THUS, WE PROVIDE BIOCHEMICAL AND FUNCTIONAL EVIDENCE THAT S1P REMARK 3 BINDS DIRECTLY TO HB BUT REQUIRES COBINDING OF 2,3-DPG TO DECREASE REMARK 3 THE PROTEIN AFFINITY FOR O2 REMARK 4 REMARK 4 5KSI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54124 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.87 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.8 REMARK 200 STARTING MODEL: 2DN2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M REMARK 280 SODIUM CACODYLATE TRIHYDRATE, PH 6.5 AND 30% PEG 8000, LIQUID REMARK 280 DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 47.97000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.04000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.97000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.04000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 O TYR A 42 O3 S1P D 202 2.00 REMARK 500 OE2 GLU C 116 O HOH C 301 2.13 REMARK 500 O HOH A 436 O HOH D 318 2.14 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 ASP A 75 63.93 -154.64 REMARK 500 ASN B 80 53.58 -145.26 REMARK 500 ASP C 75 38.77 -152.63 REMARK 500 LYS C 90 -70.84 -116.69 REMARK 500 LEU C 113 65.60 -118.76 REMARK 500 HIS D 2 71.43 -114.83 REMARK 500 ASN D 80 46.78 -145.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 488 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A 489 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH C 499 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH D 490 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH D 491 DISTANCE = 7.29 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 S1P A 202 REMARK 610 S1P C 202 REMARK 610 S1P C 203 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 87 NE2 REMARK 620 2 HEM A 201 NA 96.2 REMARK 620 3 HEM A 201 NB 99.6 87.1 REMARK 620 4 HEM A 201 NC 107.4 156.4 89.0 REMARK 620 5 HEM A 201 ND 104.5 87.6 155.7 86.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 92 NE2 REMARK 620 2 HEM B 201 NA 96.2 REMARK 620 3 HEM B 201 NB 97.8 88.3 REMARK 620 4 HEM B 201 NC 104.6 159.1 89.9 REMARK 620 5 HEM B 201 ND 99.5 88.1 162.6 87.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM C 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 87 NE2 REMARK 620 2 HEM C 201 NA 97.5 REMARK 620 3 HEM C 201 NB 98.5 88.2 REMARK 620 4 HEM C 201 NC 106.2 156.3 86.8 REMARK 620 5 HEM C 201 ND 105.6 87.4 155.9 87.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM D 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 92 NE2 REMARK 620 2 HEM D 201 NA 92.9 REMARK 620 3 HEM D 201 NB 99.4 87.6 REMARK 620 4 HEM D 201 NC 105.1 162.0 90.0 REMARK 620 5 HEM D 201 ND 98.2 88.5 162.1 88.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue S1P A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue S1P A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DG2 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue S1P C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue S1P C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue S1P D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DG2 D 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KSJ RELATED DB: PDB DBREF 5KSI A 1 141 UNP P69905 HBA_HUMAN 2 142 DBREF 5KSI B 1 146 UNP P68871 HBB_HUMAN 2 147 DBREF 5KSI C 1 141 UNP P69905 HBA_HUMAN 2 142 DBREF 5KSI D 1 146 UNP P68871 HBB_HUMAN 2 147 SEQRES 1 A 141 VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA ALA SEQRES 2 A 141 TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY ALA SEQRES 3 A 141 GLU ALA LEU GLU ARG MET PHE LEU SER PHE PRO THR THR SEQRES 4 A 141 LYS THR TYR PHE PRO HIS PHE ASP LEU SER HIS GLY SER SEQRES 5 A 141 ALA GLN VAL LYS GLY HIS GLY LYS LYS VAL ALA ASP ALA SEQRES 6 A 141 LEU THR ASN ALA VAL ALA HIS VAL ASP ASP MET PRO ASN SEQRES 7 A 141 ALA LEU SER ALA LEU SER ASP LEU HIS ALA HIS LYS LEU SEQRES 8 A 141 ARG VAL ASP PRO VAL ASN PHE LYS LEU LEU SER HIS CYS SEQRES 9 A 141 LEU LEU VAL THR LEU ALA ALA HIS LEU PRO ALA GLU PHE SEQRES 10 A 141 THR PRO ALA VAL HIS ALA SER LEU ASP LYS PHE LEU ALA SEQRES 11 A 141 SER VAL SER THR VAL LEU THR SER LYS TYR ARG SEQRES 1 B 146 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 B 146 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 B 146 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 B 146 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 B 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 B 146 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 B 146 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 B 146 HIS CYS ASP LYS LEU HIS VAL ASP PRO GLU ASN PHE ARG SEQRES 9 B 146 LEU LEU GLY ASN VAL LEU VAL CYS VAL LEU ALA HIS HIS SEQRES 10 B 146 PHE GLY LYS GLU PHE THR PRO PRO VAL GLN ALA ALA TYR SEQRES 11 B 146 GLN LYS VAL VAL ALA GLY VAL ALA ASN ALA LEU ALA HIS SEQRES 12 B 146 LYS TYR HIS SEQRES 1 C 141 VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA ALA SEQRES 2 C 141 TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY ALA SEQRES 3 C 141 GLU ALA LEU GLU ARG MET PHE LEU SER PHE PRO THR THR SEQRES 4 C 141 LYS THR TYR PHE PRO HIS PHE ASP LEU SER HIS GLY SER SEQRES 5 C 141 ALA GLN VAL LYS GLY HIS GLY LYS LYS VAL ALA ASP ALA SEQRES 6 C 141 LEU THR ASN ALA VAL ALA HIS VAL ASP ASP MET PRO ASN SEQRES 7 C 141 ALA LEU SER ALA LEU SER ASP LEU HIS ALA HIS LYS LEU SEQRES 8 C 141 ARG VAL ASP PRO VAL ASN PHE LYS LEU LEU SER HIS CYS SEQRES 9 C 141 LEU LEU VAL THR LEU ALA ALA HIS LEU PRO ALA GLU PHE SEQRES 10 C 141 THR PRO ALA VAL HIS ALA SER LEU ASP LYS PHE LEU ALA SEQRES 11 C 141 SER VAL SER THR VAL LEU THR SER LYS TYR ARG SEQRES 1 D 146 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 D 146 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 D 146 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 D 146 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 D 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 D 146 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 D 146 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 D 146 HIS CYS ASP LYS LEU HIS VAL ASP PRO GLU ASN PHE ARG SEQRES 9 D 146 LEU LEU GLY ASN VAL LEU VAL CYS VAL LEU ALA HIS HIS SEQRES 10 D 146 PHE GLY LYS GLU PHE THR PRO PRO VAL GLN ALA ALA TYR SEQRES 11 D 146 GLN LYS VAL VAL ALA GLY VAL ALA ASN ALA LEU ALA HIS SEQRES 12 D 146 LYS TYR HIS HET HEM A 201 43 HET S1P A 202 11 HET S1P A 203 25 HET HEM B 201 43 HET DG2 B 202 15 HET HEM C 201 43 HET S1P C 202 7 HET S1P C 203 16 HET HEM D 201 43 HET S1P D 202 25 HET DG2 D 203 15 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM S1P (2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YL HETNAM 2 S1P DIHYDROGEN PHOSPHATE HETNAM DG2 (2R)-2,3-DIPHOSPHOGLYCERIC ACID HETSYN HEM HEME HETSYN S1P SPHINGOSINE 1-PHOSPHATE HETSYN DG2 2,3-BISPHOSPHOGLYCERIC ACID; 2,3-BISPHOSPHOGLYCERATE; HETSYN 2 DG2 2,3-BPG; 2,3-DIPHOSPHOGLYCERIC ACID; 2,3- HETSYN 3 DG2 DIPHOSPHOGLYCERATE; 2,3-DPG; (2~{R})-2,3- HETSYN 4 DG2 DIPHOSPHONOOXYPROPANOIC ACID FORMUL 5 HEM 4(C34 H32 FE N4 O4) FORMUL 6 S1P 5(C18 H38 N O5 P) FORMUL 9 DG2 2(C3 H8 O10 P2) FORMUL 16 HOH *784(H2 O) HELIX 1 AA1 SER A 3 GLY A 18 1 16 HELIX 2 AA2 HIS A 20 PHE A 36 1 17 HELIX 3 AA3 PRO A 37 PHE A 43 5 7 HELIX 4 AA4 SER A 52 HIS A 72 1 21 HELIX 5 AA5 ASP A 75 LEU A 80 1 6 HELIX 6 AA6 LEU A 80 LYS A 90 1 11 HELIX 7 AA7 VAL A 96 LEU A 113 1 18 HELIX 8 AA8 THR A 118 SER A 138 1 21 HELIX 9 AA9 THR B 4 GLY B 16 1 13 HELIX 10 AB1 ASN B 19 TYR B 35 1 17 HELIX 11 AB2 PRO B 36 GLY B 46 5 11 HELIX 12 AB3 THR B 50 ASN B 57 1 8 HELIX 13 AB4 ASN B 57 LEU B 75 1 19 HELIX 14 AB5 ALA B 76 LEU B 78 5 3 HELIX 15 AB6 ASN B 80 LYS B 95 1 16 HELIX 16 AB7 PRO B 100 GLY B 119 1 20 HELIX 17 AB8 LYS B 120 PHE B 122 5 3 HELIX 18 AB9 THR B 123 HIS B 143 1 21 HELIX 19 AC1 SER C 3 GLY C 18 1 16 HELIX 20 AC2 HIS C 20 PHE C 36 1 17 HELIX 21 AC3 PRO C 37 PHE C 43 5 7 HELIX 22 AC4 SER C 52 HIS C 72 1 21 HELIX 23 AC5 ASP C 75 LEU C 80 1 6 HELIX 24 AC6 LEU C 80 LYS C 90 1 11 HELIX 25 AC7 VAL C 96 LEU C 113 1 18 HELIX 26 AC8 THR C 118 SER C 138 1 21 HELIX 27 AC9 THR D 4 GLY D 16 1 13 HELIX 28 AD1 ASN D 19 TYR D 35 1 17 HELIX 29 AD2 PRO D 36 GLY D 46 5 11 HELIX 30 AD3 THR D 50 GLY D 56 1 7 HELIX 31 AD4 ASN D 57 LEU D 75 1 19 HELIX 32 AD5 ALA D 76 ASP D 79 5 4 HELIX 33 AD6 ASN D 80 PHE D 85 1 6 HELIX 34 AD7 PHE D 85 LYS D 95 1 11 HELIX 35 AD8 PRO D 100 GLY D 119 1 20 HELIX 36 AD9 LYS D 120 PHE D 122 5 3 HELIX 37 AE1 THR D 123 HIS D 143 1 21 LINK NE2 HIS A 87 FE HEM A 201 1555 1555 2.09 LINK NE2 HIS B 92 FE HEM B 201 1555 1555 2.07 LINK NE2 HIS C 87 FE HEM C 201 1555 1555 2.09 LINK NE2 HIS D 92 FE HEM D 201 1555 1555 2.09 SITE 1 AC1 23 TYR A 42 PHE A 43 HIS A 45 PHE A 46 SITE 2 AC1 23 HIS A 58 LYS A 61 LEU A 83 LEU A 86 SITE 3 AC1 23 HIS A 87 LEU A 91 VAL A 93 ASN A 97 SITE 4 AC1 23 PHE A 98 LEU A 101 LEU A 136 HOH A 315 SITE 5 AC1 23 HOH A 320 HOH A 332 HOH A 334 HOH A 349 SITE 6 AC1 23 HOH A 368 LYS D 17 S1P D 202 SITE 1 AC2 7 PHE A 36 LYS A 99 LEU A 100 HIS A 103 SITE 2 AC2 7 HOH A 302 HOH A 310 ASN B 108 SITE 1 AC3 14 THR A 41 TYR A 42 PRO A 44 HIS A 45 SITE 2 AC3 14 LYS A 90 LEU A 91 ARG A 92 ARG D 40 SITE 3 AC3 14 PHE D 41 LEU D 96 HIS D 97 HEM D 201 SITE 4 AC3 14 S1P D 202 HOH D 307 SITE 1 AC4 12 LYS A 56 HIS B 63 LYS B 66 VAL B 67 SITE 2 AC4 12 LEU B 91 HIS B 92 LEU B 96 ASN B 102 SITE 3 AC4 12 PHE B 103 LEU B 141 HOH B 362 HOH B 394 SITE 1 AC5 7 LYS B 82 HOH B 329 HOH B 330 HOH B 342 SITE 2 AC5 7 HOH B 358 DG2 D 203 HOH D 338 SITE 1 AC6 20 MET C 32 TYR C 42 PHE C 43 HIS C 45 SITE 2 AC6 20 PHE C 46 HIS C 58 LYS C 61 LEU C 83 SITE 3 AC6 20 LEU C 86 HIS C 87 LEU C 91 VAL C 93 SITE 4 AC6 20 ASN C 97 PHE C 98 LEU C 101 LEU C 136 SITE 5 AC6 20 S1P C 203 HOH C 336 HOH C 360 HOH C 403 SITE 1 AC7 10 PHE C 36 LYS C 99 LEU C 100 HIS C 103 SITE 2 AC7 10 HOH C 304 HOH C 355 HOH C 361 HOH C 390 SITE 3 AC7 10 ASN D 108 GLN D 131 SITE 1 AC8 9 ARG B 40 HIS B 97 THR C 41 TYR C 42 SITE 2 AC8 9 PRO C 44 LYS C 90 LEU C 91 ARG C 92 SITE 3 AC8 9 HEM C 201 SITE 1 AC9 21 S1P A 203 HIS C 72 HOH C 331 PHE D 41 SITE 2 AC9 21 PHE D 42 HIS D 63 LYS D 66 VAL D 67 SITE 3 AC9 21 LEU D 91 HIS D 92 LEU D 96 ASN D 102 SITE 4 AC9 21 PHE D 103 LEU D 141 S1P D 202 HOH D 302 SITE 5 AC9 21 HOH D 313 HOH D 316 HOH D 341 HOH D 344 SITE 6 AC9 21 HOH D 392 SITE 1 AD1 18 THR A 41 TYR A 42 HIS A 45 LYS A 90 SITE 2 AD1 18 LEU A 91 HEM A 201 S1P A 203 HIS C 72 SITE 3 AD1 18 ARG D 40 PHE D 41 LEU D 96 HIS D 97 SITE 4 AD1 18 LYS D 120 HEM D 201 HOH D 301 HOH D 316 SITE 5 AD1 18 HOH D 344 HOH D 385 SITE 1 AD2 9 LYS B 82 DG2 B 202 HOH B 330 VAL D 1 SITE 2 AD2 9 LYS D 82 HOH D 334 HOH D 337 HOH D 338 SITE 3 AD2 9 HOH D 403 CRYST1 95.940 98.080 65.140 90.00 90.00 90.00 P 21 21 2 8 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 0.010423 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015352 0.00000