0.012315 0.000000 0.000000 0.000000 0.012315 0.000000 0.000000 0.000000 0.011008 0.00000 0.00000 0.00000 Chattopadhyay, D. Langsley, G. Carson, M. Recacha, R. DeLucas, L. Smith, C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 81.200 81.200 90.840 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C10 H15 N5 O11 P2 443.201 n GUANOSINE-5'-DIPHOSPHATE RNA linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking Mg 2 24.305 MAGNESIUM ION non-polymer C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 56 937 944 10.1107/S0907444900007575 10944329 Structure of the nucleotide-binding domain of Plasmodium falciparum rab6 in the GDP-bound form. 2000 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 CCD 1999-02-25 MARRESEARCH MAD M x-ray 1 0.9789 1.0 0.9770 1.0 0.9791 1.0 APS 0.9789, 0.9770, 0.9791 SYNCHROTRON APS 18737.814 RAB6 GTPASE 1 man polymer 24.305 MAGNESIUM ION 1 syn non-polymer 443.201 GUANOSINE-5'-DIPHOSPHATE 1 syn non-polymer 18.015 water 63 nat water no yes KYKLVFLGEQAVGKTSIITRF(MSE)YDTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAA AIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEG(MSE)QKAQEYNT(MSE)FHETSAKAG HNIKVLFKKTASKL KYKLVFLGEQAVGKTSIITRFMYDTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVV YDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTAS KL A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n malaria parasite P. falciparum Plasmodium Escherichia sample 5833 Plasmodium falciparum 562 Escherichia coli PET21 1 3.9 68.0 VAPOR DIFFUSION, HANGING DROP 6.5 sodium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K 295 pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues software repository Initial release Version format compliance Version format compliance Advisory Refinement description 1 0 2000-08-30 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 RCSB Y RCSB 1999-10-06 REL REL MG MAGNESIUM ION GDP GUANOSINE-5'-DIPHOSPHATE HOH water MG 300 2 MG MG 300 A GDP 201 3 GDP GDP 201 A HOH 1 4 HOH HOH 301 A HOH 2 4 HOH HOH 302 A HOH 3 4 HOH HOH 303 A HOH 4 4 HOH HOH 304 A HOH 5 4 HOH HOH 305 A HOH 6 4 HOH HOH 306 A HOH 7 4 HOH HOH 307 A HOH 8 4 HOH HOH 308 A HOH 9 4 HOH HOH 309 A HOH 10 4 HOH HOH 310 A HOH 11 4 HOH HOH 311 A HOH 12 4 HOH HOH 312 A HOH 13 4 HOH HOH 313 A HOH 14 4 HOH HOH 314 A HOH 15 4 HOH HOH 315 A HOH 16 4 HOH HOH 316 A HOH 17 4 HOH HOH 317 A HOH 18 4 HOH HOH 318 A HOH 19 4 HOH HOH 319 A HOH 20 4 HOH HOH 320 A HOH 21 4 HOH HOH 321 A HOH 22 4 HOH HOH 322 A HOH 23 4 HOH HOH 323 A HOH 24 4 HOH HOH 324 A HOH 25 4 HOH HOH 325 A HOH 26 4 HOH HOH 326 A HOH 27 4 HOH HOH 327 A HOH 28 4 HOH HOH 328 A HOH 29 4 HOH HOH 329 A HOH 30 4 HOH HOH 330 A HOH 31 4 HOH HOH 331 A HOH 32 4 HOH HOH 332 A HOH 33 4 HOH HOH 333 A HOH 34 4 HOH HOH 334 A HOH 35 4 HOH HOH 335 A HOH 36 4 HOH HOH 336 A HOH 37 4 HOH HOH 337 A HOH 38 4 HOH HOH 338 A HOH 39 4 HOH HOH 339 A HOH 40 4 HOH HOH 340 A HOH 41 4 HOH HOH 341 A HOH 42 4 HOH HOH 342 A HOH 43 4 HOH HOH 343 A HOH 44 4 HOH HOH 344 A HOH 45 4 HOH HOH 345 A HOH 46 4 HOH HOH 346 A HOH 47 4 HOH HOH 347 A HOH 48 4 HOH HOH 348 A HOH 49 4 HOH HOH 349 A HOH 50 4 HOH HOH 350 A HOH 51 4 HOH HOH 351 A HOH 52 4 HOH HOH 352 A HOH 53 4 HOH HOH 353 A HOH 54 4 HOH HOH 354 A HOH 55 4 HOH HOH 355 A HOH 56 4 HOH HOH 356 A HOH 57 4 HOH HOH 357 A HOH 58 4 HOH HOH 358 A HOH 59 4 HOH HOH 359 A HOH 60 4 HOH HOH 360 A HOH 61 4 HOH HOH 361 A HOH 62 4 HOH HOH 362 A HOH 63 4 HOH HOH 363 A LYS 11 n 1 LYS 11 A TYR 12 n 2 TYR 12 A LYS 13 n 3 LYS 13 A LEU 14 n 4 LEU 14 A VAL 15 n 5 VAL 15 A PHE 16 n 6 PHE 16 A LEU 17 n 7 LEU 17 A GLY 18 n 8 GLY 18 A GLU 19 n 9 GLU 19 A GLN 20 n 10 GLN 20 A ALA 21 n 11 ALA 21 A VAL 22 n 12 VAL 22 A GLY 23 n 13 GLY 23 A LYS 24 n 14 LYS 24 A THR 25 n 15 THR 25 A SER 26 n 16 SER 26 A ILE 27 n 17 ILE 27 A ILE 28 n 18 ILE 28 A THR 29 n 19 THR 29 A ARG 30 n 20 ARG 30 A PHE 31 n 21 PHE 31 A MSE 32 n 22 MSE 32 A TYR 33 n 23 TYR 33 A ASP 34 n 24 ASP 34 A THR 35 n 25 THR 35 A PHE 36 n 26 PHE 36 A ASP 37 n 27 ASP 37 A ASN 38 n 28 ASN 38 A ASN 39 n 29 ASN 39 A TYR 40 n 30 TYR 40 A GLN 41 n 31 GLN 41 A SER 42 n 32 SER 42 A THR 43 n 33 THR 43 A ILE 44 n 34 ILE 44 A GLY 45 n 35 GLY 45 A ILE 46 n 36 ILE 46 A ASP 47 n 37 ASP 47 A PHE 48 n 38 PHE 48 A LEU 49 n 39 LEU 49 A SER 50 n 40 SER 50 A LYS 51 n 41 LYS 51 A THR 52 n 42 THR 52 A LEU 53 n 43 LEU 53 A TYR 54 n 44 TYR 54 A LEU 55 n 45 LEU 55 A ASP 56 n 46 ASP 56 A GLU 57 n 47 GLU 57 A GLY 58 n 48 GLY 58 A PRO 59 n 49 PRO 59 A VAL 60 n 50 VAL 60 A ARG 61 n 51 ARG 61 A LEU 62 n 52 LEU 62 A GLN 63 n 53 GLN 63 A LEU 64 n 54 LEU 64 A TRP 65 n 55 TRP 65 A ASP 66 n 56 ASP 66 A THR 67 n 57 THR 67 A ALA 68 n 58 ALA 68 A GLY 69 n 59 GLY 69 A GLN 70 n 60 GLN 70 A GLU 71 n 61 GLU 71 A ARG 72 n 62 ARG 72 A PHE 73 n 63 PHE 73 A ARG 74 n 64 ARG 74 A SER 75 n 65 SER 75 A LEU 76 n 66 LEU 76 A ILE 77 n 67 ILE 77 A PRO 78 n 68 PRO 78 A SER 79 n 69 SER 79 A TYR 80 n 70 TYR 80 A ILE 81 n 71 ILE 81 A ARG 82 n 72 ARG 82 A ASP 83 n 73 ASP 83 A SER 84 n 74 SER 84 A ALA 85 n 75 ALA 85 A ALA 86 n 76 ALA 86 A ALA 87 n 77 ALA 87 A ILE 88 n 78 ILE 88 A VAL 89 n 79 VAL 89 A VAL 90 n 80 VAL 90 A TYR 91 n 81 TYR 91 A ASP 92 n 82 ASP 92 A ILE 93 n 83 ILE 93 A THR 94 n 84 THR 94 A ASN 95 n 85 ASN 95 A ARG 96 n 86 ARG 96 A GLN 97 n 87 GLN 97 A SER 98 n 88 SER 98 A PHE 99 n 89 PHE 99 A GLU 100 n 90 GLU 100 A ASN 101 n 91 ASN 101 A THR 102 n 92 THR 102 A THR 103 n 93 THR 103 A LYS 104 n 94 LYS 104 A TRP 105 n 95 TRP 105 A ILE 106 n 96 ILE 106 A GLN 107 n 97 GLN 107 A ASP 108 n 98 ASP 108 A ILE 109 n 99 ILE 109 A LEU 110 n 100 LEU 110 A ASN 111 n 101 ASN 111 A GLU 112 n 102 GLU 112 A ARG 113 n 103 ARG 113 A GLY 114 n 104 GLY 114 A LYS 115 n 105 LYS 115 A ASP 116 n 106 ASP 116 A VAL 117 n 107 VAL 117 A ILE 118 n 108 ILE 118 A ILE 119 n 109 ILE 119 A ALA 120 n 110 ALA 120 A LEU 121 n 111 LEU 121 A VAL 122 n 112 VAL 122 A GLY 123 n 113 GLY 123 A ASN 124 n 114 ASN 124 A LYS 125 n 115 LYS 125 A THR 126 n 116 THR 126 A ASP 127 n 117 ASP 127 A LEU 128 n 118 LEU 128 A GLY 129 n 119 GLY 129 A ASP 130 n 120 ASP 130 A LEU 131 n 121 LEU 131 A ARG 132 n 122 ARG 132 A LYS 133 n 123 LYS 133 A VAL 134 n 124 VAL 134 A THR 135 n 125 THR 135 A TYR 136 n 126 TYR 136 A GLU 137 n 127 GLU 137 A GLU 138 n 128 GLU 138 A GLY 139 n 129 GLY 139 A MSE 140 n 130 MSE 140 A GLN 141 n 131 GLN 141 A LYS 142 n 132 LYS 142 A ALA 143 n 133 ALA 143 A GLN 144 n 134 GLN 144 A GLU 145 n 135 GLU 145 A TYR 146 n 136 TYR 146 A ASN 147 n 137 ASN 147 A THR 148 n 138 THR 148 A MSE 149 n 139 MSE 149 A PHE 150 n 140 PHE 150 A HIS 151 n 141 HIS 151 A GLU 152 n 142 GLU 152 A THR 153 n 143 THR 153 A SER 154 n 144 SER 154 A ALA 155 n 145 ALA 155 A LYS 156 n 146 LYS 156 A ALA 157 n 147 ALA 157 A GLY 158 n 148 GLY 158 A HIS 159 n 149 HIS 159 A ASN 160 n 150 ASN 160 A ILE 161 n 151 ILE 161 A LYS 162 n 152 LYS 162 A VAL 163 n 153 VAL 163 A LEU 164 n 154 LEU 164 A PHE 165 n 155 PHE 165 A LYS 166 n 156 LYS 166 A LYS 167 n 157 LYS 167 A THR 168 n 158 THR 168 A ALA 169 n 159 ALA 169 A SER 170 n 160 SER 170 A LYS 171 n 161 LYS 171 A LEU 172 n 162 LEU 172 A author_defined_assembly 1 monomeric A HOH 352 D O HOH 1_555 A MG 300 B MG MG 1_555 A HOH 353 D O HOH 1_555 76.9 A HOH 352 D O HOH 1_555 A MG 300 B MG MG 1_555 A HOH 350 D O HOH 1_555 159.6 A HOH 353 D O HOH 1_555 A MG 300 B MG MG 1_555 A HOH 350 D O HOH 1_555 95.1 A HOH 352 D O HOH 1_555 A MG 300 B MG MG 1_555 A THR 25 A OG1 THR 15 1_555 78.9 A HOH 353 D O HOH 1_555 A MG 300 B MG MG 1_555 A THR 25 A OG1 THR 15 1_555 87.2 A HOH 350 D O HOH 1_555 A MG 300 B MG MG 1_555 A THR 25 A OG1 THR 15 1_555 82.1 A HOH 352 D O HOH 1_555 A MG 300 B MG MG 1_555 A GDP 201 C O3B GDP 1_555 89.3 A HOH 353 D O HOH 1_555 A MG 300 B MG MG 1_555 A GDP 201 C O3B GDP 1_555 164.3 A HOH 350 D O HOH 1_555 A MG 300 B MG MG 1_555 A GDP 201 C O3B GDP 1_555 95.5 A THR 25 A OG1 THR 15 1_555 A MG 300 B MG MG 1_555 A GDP 201 C O3B GDP 1_555 82.8 A HOH 352 D O HOH 1_555 A MG 300 B MG MG 1_555 A HOH 351 D O HOH 1_555 90.1 A HOH 353 D O HOH 1_555 A MG 300 B MG MG 1_555 A HOH 351 D O HOH 1_555 90.6 A HOH 350 D O HOH 1_555 A MG 300 B MG MG 1_555 A HOH 351 D O HOH 1_555 109.0 A THR 25 A OG1 THR 15 1_555 A MG 300 B MG MG 1_555 A HOH 351 D O HOH 1_555 168.9 A GDP 201 C O3B GDP 1_555 A MG 300 B MG MG 1_555 A HOH 351 D O HOH 1_555 96.9 A MSE 32 SELENOMETHIONINE A MSE 22 MET A MSE 140 SELENOMETHIONINE A MSE 130 MET A MSE 149 SELENOMETHIONINE A MSE 139 MET 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 A O LEU 55 A O LEU 45 A N GLY 58 A N GLY 48 A N GLN 63 A N GLN 53 A O TYR 12 A O TYR 2 A N VAL 15 A N VAL 5 A O ALA 86 A O ALA 76 A N ALA 87 A N ALA 77 A O ILE 118 A O ILE 108 A N LEU 121 A N LEU 111 A O MSE 149 A O MSE 139 1 A SER 42 -9.19 138.13 1 A ASP 56 -68.81 53.17 1 A GLU 57 -165.88 -18.25 1 A ASP 83 57.77 16.36 1 A ASP 116 -85.01 42.99 1 A LYS 125 76.74 45.06 PROTEIN_REP.PARAM PROTEIN.TOP ION.PARAM GDP_F.PARAM WATER_REP.PARA 34.3 0.00 0.00 0.00 0.00 0.00 0.00 F48 has been fixed because it lies on a two fold symmetry element. 0.246 0.007 0.214 2.30 9.94 1391 13831 13776 10.1 99.6 RANDOM 1501218.10 1501218.10 0.00 1 RESTRAINED THROUGHOUT 3.0 MLF FLAT MODEL 34.4068 0.371 0.34 0.31 10.00 0.24 0.22 2.30 9.94 63 1403 29 0 1311 0.006 1.2 23.3 0.63 3.44 1.50 3.51 2.00 1.82 2.00 2.84 2.50 0.266 0.017 0.25 2.44 234 2022 6 10.4 99.8 20.0 2.2 20.0 1D5C 15971 15968 0.0 0.087 1 25.4 18.4 100.0 0.28 2.3 2.4 12.6 1560 18.7 100.0 data collection MAR345 data reduction d*TREK phasing SOLVE refinement CNS 0.9 data scaling d*TREK RAB6 GTPASE CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM RAB6 COMPLEXED WITH GDP 1 N N 2 N N 3 N N 4 N N A GLY 23 A GLY 13 HELX_P A ASP 34 A ASP 24 1 1 12 A GLN 70 A GLN 60 HELX_P A SER 75 A SER 65 5 2 6 A LEU 76 A LEU 66 HELX_P A ARG 82 A ARG 72 1 3 7 A ASN 95 A ASN 85 HELX_P A ASN 101 A ASN 91 1 4 7 A ASN 101 A ASN 91 HELX_P A GLY 114 A GLY 104 1 5 14 A LYS 125 A LYS 115 HELX_P A GLY 129 A GLY 119 5 6 5 A LEU 128 A LEU 118 HELX_P A ARG 132 A ARG 122 5 7 5 A THR 135 A THR 125 HELX_P A TYR 146 A TYR 136 1 8 12 A ILE 161 A ILE 151 HELX_P A LYS 171 A LYS 161 1 9 11 covale 1.329 A PHE 31 A C PHE 21 1_555 A MSE 32 A N MSE 22 1_555 covale 1.330 A MSE 32 A C MSE 22 1_555 A TYR 33 A N TYR 23 1_555 covale 1.328 A GLY 139 A C GLY 129 1_555 A MSE 140 A N MSE 130 1_555 covale 1.328 A MSE 140 A C MSE 130 1_555 A GLN 141 A N GLN 131 1_555 covale 1.329 A THR 148 A C THR 138 1_555 A MSE 149 A N MSE 139 1_555 covale 1.330 A MSE 149 A C MSE 139 1_555 A PHE 150 A N PHE 140 1_555 metalc 2.137 A MG 300 B MG MG 1_555 A HOH 352 D O HOH 1_555 metalc 2.110 A MG 300 B MG MG 1_555 A HOH 353 D O HOH 1_555 metalc 2.042 A MG 300 B MG MG 1_555 A HOH 350 D O HOH 1_555 metalc 2.179 A MG 300 B MG MG 1_555 A THR 25 A OG1 THR 15 1_555 metalc 2.072 A MG 300 B MG MG 1_555 A GDP 201 C O3B GDP 1_555 metalc 2.001 A MG 300 B MG MG 1_555 A HOH 351 D O HOH 1_555 ENDOCYTOSIS/EXOCYTOSIS G-PROTEIN, GTPASE, RAB, RAB6, VESICULAR TRAFFICKING, ENDOCYTOSIS-EXOCYTOSIS COMPLEX Q26000_PLAFA UNP 1 Q26000 11 172 1D5C 11 172 Q26000 A 1 1 162 1 MET MODIFIED RESIDUE MSE 32 1D5C A Q26000 UNP 32 22 1 MET MODIFIED RESIDUE MSE 140 1D5C A Q26000 UNP 140 130 1 MET MODIFIED RESIDUE MSE 149 1D5C A Q26000 UNP 149 139 6 anti-parallel parallel parallel parallel parallel A ASP 47 A ASP 37 A LEU 55 A LEU 45 A GLY 58 A GLY 48 A ASP 66 A ASP 56 A TYR 12 A TYR 2 A LEU 17 A LEU 7 A ALA 86 A ALA 76 A ASP 92 A ASP 82 A ILE 118 A ILE 108 A ASN 124 A ASN 114 A MSE 149 A MSE 139 A GLU 152 A GLU 142 BINDING SITE FOR RESIDUE MG A 300 Software 6 BINDING SITE FOR RESIDUE GDP A 201 Software 23 A THR 25 A THR 15 6 1_555 A GDP 201 C GDP 6 1_555 A HOH 350 D HOH 6 1_555 A HOH 351 D HOH 6 1_555 A HOH 352 D HOH 6 1_555 A HOH 353 D HOH 6 1_555 A GLN 20 A GLN 10 23 1_555 A ALA 21 A ALA 11 23 1_555 A VAL 22 A VAL 12 23 1_555 A GLY 23 A GLY 13 23 1_555 A LYS 24 A LYS 14 23 1_555 A THR 25 A THR 15 23 1_555 A SER 26 A SER 16 23 1_555 A PHE 36 A PHE 26 23 1_555 A TYR 40 A TYR 30 23 1_555 A SER 42 A SER 32 23 1_555 A ASN 124 A ASN 114 23 1_555 A LYS 125 A LYS 115 23 1_555 A ASP 127 A ASP 117 23 1_555 A SER 154 A SER 144 23 1_555 A ALA 155 A ALA 145 23 1_555 A LYS 156 A LYS 146 23 1_555 A MG 300 B MG 23 1_555 A HOH 326 D HOH 23 1_555 A HOH 332 D HOH 23 1_555 A HOH 344 D HOH 23 1_555 A HOH 350 D HOH 23 1_555 A HOH 351 D HOH 23 1_555 A HOH 352 D HOH 23 1_555 96 P 43 21 2