0.047971 0.027273 0.013306 0.000000 0.055015 0.017373 0.000000 0.000000 0.038926 0.00000 0.00000 0.00000 Prive, G.G. Anderson, D.H. Wesson, L. Cascio, D. Eisenberg, D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 102.40 95.33 119.62 20.846 20.909 27.057 C2 H4 O 44.053 ACETYL GROUP non-polymer Cl -1 35.453 CHLORIDE ION non-polymer C2 H7 N O 61.083 ETHANOLAMINE L-peptide COOH carboxy terminus C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C6 H14 O2 118.174 (4S)-2-METHYL-2,4-PENTANEDIOL non-polymer C6 H14 O2 118.174 (4R)-2-METHYLPENTANE-2,4-DIOL non-polymer N 1 N C N 2 N O N 3 N C N 4 N H N 5 N H N 6 N H N 7 N H N 8 N CL N 9 N C N 10 N N N 11 N C N 12 N O N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N N N 21 S C N 22 N C N 23 N O N 24 N C N 25 N C N 26 N C N 27 N O N 28 N O N 29 N O N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N N N 40 N C N 41 N C N 42 N O N 43 N O N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N O N 50 N H N 51 N H N 52 N N N 53 S C N 54 N C N 55 N O N 56 N C N 57 N C N 58 N C N 59 N C N 60 N O N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 S C N 76 N C N 77 N O N 78 N C N 79 N C N 80 N C N 81 N C N 82 N N N 83 N O N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N C N 100 N C N 101 N O N 102 N C N 103 N C N 104 S C N 105 N O N 106 N C N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N C N 122 N C N 123 N O N 124 N C N 125 N C N 126 R C N 127 N O N 128 N C N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N doub N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N doub N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N doub N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing US Protein Sci. PRCIEI 0795 0961-8368 8 1400 1409 10422828 Packed protein bilayers in the 0.90 A resolution structure of a designed alpha helical bundle. 1999 US Protein Sci. PRCIEI 0795 0961-8368 8 1410 Centrosymmetric Bilayers in the 0.75A Resolution Structure of a Designed Alpha- Helical Peptide, D, L-Alpha-1 1999 US Science SCIEAS 0038 0036-8075 249 543 Crystal Structure of Alpha-1: Implications for Protein Design 1990 US Proteins PSFGEY 0867 0887-3585 1 16 The Design, Synthesis, and Crystallization of an Alpha-Helical Peptide 1986 10.2210/pdb1byz/pdb pdb_00001byz 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 IMAGE PLATE 1994-11-15 MARRESEARCH SI SINGLE WAVELENGTH M x-ray 1 0.9 1.0 X12C NSLS 0.9 SYNCHROTRON NSLS BEAMLINE X12C N TERMINI ARE ACETYLATED 1441.775 PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1") 4 syn polymer 61.083 ETHANOLAMINE 2 syn non-polymer 118.174 (4S)-2-METHYL-2,4-PENTANEDIOL 3 syn non-polymer 35.453 CHLORIDE ION 1 syn non-polymer 118.174 (4R)-2-METHYLPENTANE-2,4-DIOL 1 syn non-polymer 18.015 water 30 nat water no yes (ACE)ELLKKLLEELKG XELLKKLLEELKG A,B,C,D polypeptide(L) n n n n n n n n n n n n n 1 1.69 27.13 SNB SUCCESS RATE WAS 5%. VAPOR DIFFUSION, SITTING DROP 8.0 91% 2-METHYL-2,4-PENTANEDIOL, 78mM TRIETHANOLAMINE-HCL pH8, 52mM ETHANOLAMINE-HCL pH9.75, pH 8.0, VAPOR DIFFUSION, SITTING DROP software entity exptl_crystal pdbx_entity_src_syn atom_site atom_site_anisotrop chem_comp_atom chem_comp_bond database_2 struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Atomic model Version format compliance Refinement description Data collection Experimental preparation Source and taxonomy Structure summary Atomic model Data collection Database references Derived calculations Refinement description 1 0 1998-10-28 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 1 4 2018-05-30 2 0 2023-11-15 2 1 2024-04-03 _entity.src_method _exptl_crystal.density_Matthews _exptl_crystal.density_percent_sol _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_atom_id _atom_site_anisotrop.U[1][1] _atom_site_anisotrop.U[2][2] _atom_site_anisotrop.U[3][3] _atom_site_anisotrop.pdbx_auth_atom_id _atom_site_anisotrop.pdbx_label_atom_id _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y RCSB 1998-10-20 REL REL ETA ETHANOLAMINE MPD (4S)-2-METHYL-2,4-PENTANEDIOL CL CHLORIDE ION MRD (4R)-2-METHYLPENTANE-2,4-DIOL HOH water 32630 synthetic construct sample MPD 513 IS BUILT IN TWO OVERLAPPING CONFORMATIONS. ALL THE WATERS ARE IN SINGLE SITES. 448 random atoms Other in silico model ETA 502 2 ETA ETA 502 A MPD 513 3 MPD MPD 513 A MPD 511 3 MPD MPD 511 B CL 520 4 CL CL 520 C ETA 501 2 ETA ETA 501 C MPD 510 5 MRD MRD 510 D MPD 512 3 MPD MPD 512 D HOH 602 6 HOH HOH 602 A HOH 603 6 HOH HOH 603 A HOH 604 6 HOH HOH 604 A HOH 605 6 HOH HOH 605 A HOH 619 6 HOH HOH 619 A HOH 623 6 HOH HOH 623 A HOH 606 6 HOH HOH 606 B HOH 614 6 HOH HOH 614 B HOH 629 6 HOH HOH 629 B HOH 630 6 HOH HOH 630 B HOH 632 6 HOH HOH 632 B HOH 633 6 HOH HOH 633 B HOH 634 6 HOH HOH 634 B HOH 610 6 HOH HOH 610 C HOH 613 6 HOH HOH 613 C HOH 616 6 HOH HOH 616 C HOH 618 6 HOH HOH 618 C HOH 631 6 HOH HOH 631 C HOH 601 6 HOH HOH 601 D HOH 607 6 HOH HOH 607 D HOH 608 6 HOH HOH 608 D HOH 609 6 HOH HOH 609 D HOH 611 6 HOH HOH 611 D HOH 612 6 HOH HOH 612 D HOH 615 6 HOH HOH 615 D HOH 617 6 HOH HOH 617 D HOH 621 6 HOH HOH 621 D HOH 624 6 HOH HOH 624 D HOH 627 6 HOH HOH 627 D HOH 628 6 HOH HOH 628 D ACE 100 n 1 ACE 100 A GLU 101 n 2 GLU 101 A LEU 102 n 3 LEU 102 A LEU 103 n 4 LEU 103 A LYS 104 n 5 LYS 104 A LYS 105 n 6 LYS 105 A LEU 106 n 7 LEU 106 A LEU 107 n 8 LEU 107 A GLU 108 n 9 GLU 108 A GLU 109 n 10 GLU 109 A LEU 110 n 11 LEU 110 A LYS 111 n 12 LYS 111 A GLY 112 n 13 GLY 112 A ACE 200 n 1 ACE 200 B GLU 201 n 2 GLU 201 B LEU 202 n 3 LEU 202 B LEU 203 n 4 LEU 203 B LYS 204 n 5 LYS 204 B LYS 205 n 6 LYS 205 B LEU 206 n 7 LEU 206 B LEU 207 n 8 LEU 207 B GLU 208 n 9 GLU 208 B GLU 209 n 10 GLU 209 B LEU 210 n 11 LEU 210 B LYS 211 n 12 LYS 211 B GLY 212 n 13 GLY 212 B ACE 300 n 1 ACE 300 C GLU 301 n 2 GLU 301 C LEU 302 n 3 LEU 302 C LEU 303 n 4 LEU 303 C LYS 304 n 5 LYS 304 C LYS 305 n 6 LYS 305 C LEU 306 n 7 LEU 306 C LEU 307 n 8 LEU 307 C GLU 308 n 9 GLU 308 C GLU 309 n 10 GLU 309 C LEU 310 n 11 LEU 310 C LYS 311 n 12 LYS 311 C GLY 312 n 13 GLY 312 C ACE 400 n 1 ACE 400 D GLU 401 n 2 GLU 401 D LEU 402 n 3 LEU 402 D LEU 403 n 4 LEU 403 D LYS 404 n 5 LYS 404 D LYS 405 n 6 LYS 405 D LEU 406 n 7 LEU 406 D LEU 407 n 8 LEU 407 D GLU 408 n 9 GLU 408 D GLU 409 n 10 GLU 409 D LEU 410 n 11 LEU 410 D LYS 411 n 12 LYS 411 D GLY 412 n 13 GLY 412 D 0.081 0.086 0.08 0.085 0.098 0.105 2179 2368 9.20 10.00 21831 author_defined_assembly 4 tetrameric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 C C HZ1 HO LYS ETA 304 501 1.35 1 D D O O HOH HOH 624 628 2.18 MORE LOW-OCCUPANCY DISCRETE DISORDER COULD BE BUILT FOR SOLVENT AND PEPTIDE, BUT WOULD EXCESSIVELY INCREASE THE NUMBER OF REFINEABLE PARAMETERS. 0.105 0.086 0.085 0.90 25.7 4695 2368 23681 5898 10.00 85.9 EVERY TENTH REFLECTION SAME TEST SET FOR SHELXL-93 AND SHELXL-97 1 FREE R 2.000 DIRECT METHODS 448 RANDOM ATOMS ETHANOLAMINE AND MPD RESTRAINTS WERE DERIVED BY ANALOGY TO OTHER SIMILAR GROUPS ENGH AND HUBER MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 7 544.00 478.97 0.90 25.7 30 479 41 0 408 0.025 0.000 0.016 0.017 0.065 0.000 0.192 0.006 0.026 0.108 0.900 25.700 1BYZ 23681 1.000 0.076 1 16.3000 3.300 85.9 0.90 0.93 4.300 0.141 1 1.30 36.0 model building SHAKE phasing SnB (SNB 1.5) MILLER refinement SHELXL refinement SHELXL-97 data reduction DENZO (DENZO) data scaling SCALEPACK (DENZO) DESIGNED PEPTIDE ALPHA-1, P1 FORM 1 N N 1 N N 1 N N 1 N N 2 N N 3 N N 3 N N 4 N N 2 N N 5 N N 3 N N 6 N N 6 N N 6 N N 6 N N A GLU 101 A GLU 2 HELX_P A GLY 112 A GLY 13 1 1 12 B GLU 201 B GLU 2 HELX_P B GLY 212 B GLY 13 1 2 12 C GLU 301 C GLU 2 HELX_P C GLY 312 C GLY 13 1 3 12 D GLU 401 D GLU 2 HELX_P D GLY 412 D GLY 13 1 4 12 covale 1.348 both A ACE 100 A C ACE 1 1_555 A GLU 101 A N GLU 2 1_555 covale 1.332 both B ACE 200 B C ACE 1 1_555 B GLU 201 B N GLU 2 1_555 covale 1.345 both C ACE 300 C C ACE 1 1_555 C GLU 301 C N GLU 2 1_555 covale 1.360 both D ACE 400 D C ACE 1 1_555 D GLU 401 D N GLU 2 1_555 DE NOVO PROTEIN HELICAL BILAYER; BIOMATERIAL, DE NOVO PROTEIN 1BYZ PDB 1 1BYZ 100 112 1BYZ 100 112 1BYZ A 1 1 13 200 212 1BYZ 200 212 1BYZ B 1 1 13 300 312 1BYZ 300 312 1BYZ C 1 1 13 400 412 1BYZ 400 412 1BYZ D 1 1 13 BINDING SITE FOR RESIDUE CL C 520 C CL 520 Software 4 BINDING SITE FOR RESIDUE MRD D 510 D MRD 510 Software 4 BINDING SITE FOR RESIDUE ETA C 501 C ETA 501 Software 6 BINDING SITE FOR RESIDUE ETA A 502 A ETA 502 Software 4 BINDING SITE FOR RESIDUE MPD B 511 B MPD 511 Software 3 BINDING SITE FOR RESIDUE MPD D 512 D MPD 512 Software 4 BINDING SITE FOR RESIDUE MPD A 513 A MPD 513 Software 10 A LYS 104 A LYS 5 4 1_544 B LYS 204 B LYS 5 4 1_644 C LYS 311 C LYS 12 4 1_555 D LYS 405 D LYS 6 4 1_545 D ACE 400 D ACE 1 4 1_455 D LEU 402 D LEU 3 4 1_455 D LEU 403 D LEU 4 4 1_455 D LEU 410 D LEU 11 4 1_555 A GLU 109 A GLU 10 6 1_544 A GLY 112 A GLY 13 6 1_544 A HOH 604 L HOH 6 1_544 C GLU 301 C GLU 2 6 1_555 C LYS 304 C LYS 5 6 1_555 C GLU 308 C GLU 9 6 1_555 A LYS 105 A LYS 6 4 1_455 A GLY 112 A GLY 13 4 1_555 B GLU 209 B GLU 10 4 1_565 C GLY 312 C GLY 13 4 1_466 A LEU 103 A LEU 4 3 1_555 B LEU 210 B LEU 11 3 1_555 D MPD 512 K MPD 3 1_555 B MPD 511 G MPD 4 1_555 C LEU 310 C LEU 11 4 1_455 D LEU 402 D LEU 3 4 1_455 D GLU 409 D GLU 10 4 1_555 A ACE 100 A ACE 1 10 1_455 A LEU 102 A LEU 3 10 1_455 A GLU 109 A GLU 10 10 1_555 A LEU 110 A LEU 11 10 1_555 A HOH 619 L HOH 10 1_455 B LEU 203 B LEU 4 10 1_555 B GLU 209 B GLU 10 10 1_565 B HOH 614 M HOH 10 1_665 B HOH 633 M HOH 10 1_565 D LEU 406 D LEU 7 10 1_455 1 P 1