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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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