HEADER DE NOVO PROTEIN 26-SEP-24 9GW6 TITLE LYS9DABMC6*A 2-DELTA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACE-ASP-GLU-AIB-GLN-LEU-SER-AIB-GLN-DAB-ARG-NH2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ACE-ASP-LEU-GLN-GLN-LEU-HIS-SER-GLN-LYS-ARG-LYS-ILE-THR- COMPND 7 LEU-NH2; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS ALPHA-HELIX, DESIGN, MINIATURIZED METALLOPROTEINS, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR O.MAGLIO,A.LOMBARDI,M.CHINO,F.PIRRO REVDAT 1 28-JAN-26 9GW6 0 JRNL AUTH M.CHINO,C.CERRONE,F.PIRRO,M.DE FENZA,S.DEMESHKO,O.MAGLIO, JRNL AUTH 2 F.MEYER,A.LOMBARDI JRNL TITL IRON TO COBALT SWAPPING IN A BIOINSPIRED HEME-PEROXIDASE: JRNL TITL 2 STRUCTURAL CHARACTERIZATION AND FUNCTIONAL IMPLICATIONS JRNL REF INORG.CHEM. 2026 JRNL REFN ISSN 0020-1669 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.MAGLIO,M.CHINO,C.VICARI,V.PAVONE,R.LOURO,A.LOMBARDI REMARK 1 TITL HISTIDINE ORIENTATION IN ARTIFICIAL PEROXIDASE REGIOISOMERS REMARK 1 TITL 2 AS DETERMINED BY PARAMAGNETIC NMR SHIFTS REMARK 1 REF CHEM COMM V. 57 990 2021 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.LOMBARDI,F.NASTRI,D.MARASCO,G.DE SANCTIS,F.SINIBALDI, REMARK 1 AUTH 2 R.SANTUCCI,M.COLETTA,V.PAVONE REMARK 1 TITL DESIGN OF A NEW MIMOCHROME WITH UNIQUE TOPOLOGY REMARK 1 REF CHEMISTRY V. 9 5643 2003 REMARK 1 REFN ISSN 0947-6539 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9GW6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292141960. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.6 REMARK 210 IONIC STRENGTH : TRIFLUOROACETATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.50 MM NONE MC6*A2-DELTA, REMARK 210 50%H2O/40%TFE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D DQF-COSY; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, CYANA 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 ND DAB A 9 CGA DEU A 101 1.33 REMARK 500 NZ LYS B 9 CGD DEU A 101 1.34 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 10 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.4 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 9 AIB A 7 -9.48 -54.08 REMARK 500 11 DAB A 9 30.82 -80.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 DAB A 9 ARG A 10 11 -138.66 REMARK 500 REMARK 500 REMARK: NULL 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 1 DEU A 101 REMARK 610 2 DEU A 101 REMARK 610 3 DEU A 101 REMARK 610 4 DEU A 101 REMARK 610 5 DEU A 101 REMARK 610 6 DEU A 101 REMARK 610 7 DEU A 101 REMARK 610 8 DEU A 101 REMARK 610 9 DEU A 101 REMARK 610 10 DEU A 101 REMARK 610 11 DEU A 101 REMARK 610 12 DEU A 101 REMARK 610 13 DEU A 101 REMARK 610 14 DEU A 101 REMARK 610 15 DEU A 101 REMARK 610 16 DEU A 101 REMARK 610 17 DEU A 101 REMARK 610 18 DEU A 101 REMARK 610 19 DEU A 101 REMARK 610 20 DEU A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34962 RELATED DB: BMRB REMARK 900 LYS9DABMC6*A 2-DELTA DBREF 9GW6 A 0 11 PDB 9GW6 9GW6 0 11 DBREF 9GW6 B 0 15 PDB 9GW6 9GW6 0 15 SEQRES 1 A 12 ACE ASP GLU AIB GLN LEU SER AIB GLN DAB ARG NH2 SEQRES 1 B 16 ACE ASP LEU GLN GLN LEU HIS SER GLN LYS ARG LYS ILE SEQRES 2 B 16 THR LEU NH2 HET ACE A 0 6 HET AIB A 3 13 HET AIB A 7 13 HET DAB A 9 14 HET NH2 A 11 3 HET ACE B 0 6 HET NH2 B 15 3 HET DEU A 101 63 HET OH A 102 2 HETNAM ACE ACETYL GROUP HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM DAB 2,4-DIAMINOBUTYRIC ACID HETNAM NH2 AMINO GROUP HETNAM DEU CO(III)-(DEUTEROPORPHYRIN IX) HETNAM OH HYDROXIDE ION FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 AIB 2(C4 H9 N O2) FORMUL 1 DAB C4 H10 N2 O2 FORMUL 1 NH2 2(H2 N) FORMUL 3 DEU C30 H28 CO N4 O4 5+ FORMUL 4 OH H O 1- HELIX 1 AA1 AIB A 3 GLN A 8 1 6 HELIX 2 AA2 ASP B 1 LEU B 14 1 14 LINK C ACE A 0 N ASP A 1 1555 1555 1.33 LINK C GLU A 2 N AIB A 3 1555 1555 1.34 LINK C AIB A 3 N GLN A 4 1555 1555 1.34 LINK C SER A 6 N AIB A 7 1555 1555 1.34 LINK C AIB A 7 N GLN A 8 1555 1555 1.34 LINK C GLN A 8 N DAB A 9 1555 1555 1.34 LINK C DAB A 9 N ARG A 10 1555 1555 1.34 LINK C ARG A 10 N NH2 A 11 1555 1555 1.32 LINK C ACE B 0 N ASP B 1 1555 1555 1.33 LINK C LEU B 14 N NH2 B 15 1555 1555 1.33 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 1 2 3 7 CONECT 2 1 CONECT 3 1 4 5 6 CONECT 4 3 CONECT 5 3 CONECT 6 3 CONECT 7 1 CONECT 21 34 CONECT 34 21 35 40 CONECT 35 34 36 38 39 CONECT 36 35 37 47 CONECT 37 36 CONECT 38 35 41 42 43 CONECT 39 35 44 45 46 CONECT 40 34 CONECT 41 38 CONECT 42 38 CONECT 43 38 CONECT 44 39 CONECT 45 39 CONECT 46 39 CONECT 47 36 CONECT 85 94 CONECT 94 85 95 100 CONECT 95 94 96 98 99 CONECT 96 95 97 107 CONECT 97 96 CONECT 98 95 101 102 103 CONECT 99 95 104 105 106 CONECT 100 94 CONECT 101 98 CONECT 102 98 CONECT 103 98 CONECT 104 99 CONECT 105 99 CONECT 106 99 CONECT 107 96 CONECT 109 124 CONECT 124 109 125 131 CONECT 125 124 126 128 132 CONECT 126 125 127 138 CONECT 127 126 CONECT 128 125 129 133 134 CONECT 129 128 130 135 136 CONECT 130 129 137 CONECT 131 124 CONECT 132 125 CONECT 133 128 CONECT 134 128 CONECT 135 129 CONECT 136 129 CONECT 137 130 CONECT 138 126 CONECT 140 162 CONECT 162 140 163 164 CONECT 163 162 CONECT 164 162 CONECT 166 167 168 172 CONECT 167 166 CONECT 168 166 169 170 171 CONECT 169 168 CONECT 170 168 CONECT 171 168 CONECT 172 166 CONECT 402 419 CONECT 419 402 420 421 CONECT 420 419 CONECT 421 419 CONECT 423 442 460 461 462 CONECT 424 448 463 464 465 CONECT 425 435 466 467 468 CONECT 426 453 469 470 471 CONECT 427 428 434 472 473 CONECT 428 427 429 474 475 CONECT 429 428 430 CONECT 430 429 CONECT 431 432 454 476 477 CONECT 432 431 433 478 479 CONECT 433 432 459 CONECT 434 427 435 438 CONECT 435 425 434 436 CONECT 436 435 437 439 CONECT 437 436 438 458 CONECT 438 434 437 457 CONECT 439 436 440 480 CONECT 440 439 441 444 CONECT 441 440 442 481 CONECT 442 423 441 443 CONECT 443 442 444 445 CONECT 444 440 443 458 CONECT 445 443 446 482 CONECT 446 445 447 450 CONECT 447 446 448 483 CONECT 448 424 447 449 CONECT 449 448 450 451 CONECT 450 446 449 458 CONECT 451 449 452 484 CONECT 452 451 453 456 CONECT 453 426 452 454 CONECT 454 431 453 455 CONECT 455 454 456 457 CONECT 456 452 455 458 CONECT 457 438 455 485 CONECT 458 437 444 450 456 CONECT 459 433 CONECT 460 423 CONECT 461 423 CONECT 462 423 CONECT 463 424 CONECT 464 424 CONECT 465 424 CONECT 466 425 CONECT 467 425 CONECT 468 425 CONECT 469 426 CONECT 470 426 CONECT 471 426 CONECT 472 427 CONECT 473 427 CONECT 474 428 CONECT 475 428 CONECT 476 431 CONECT 477 431 CONECT 478 432 CONECT 479 432 CONECT 480 439 CONECT 481 441 CONECT 482 445 CONECT 483 447 CONECT 484 451 CONECT 485 457 CONECT 486 487 CONECT 487 486 MASTER 173 0 9 2 0 0 0 6 244 2 133 3 END