1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Macias, M.J. Aragon, E. Goerner, N. Zaromytidou, A. Xi, Q. Escobedo, A. Massague, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 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 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 C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H8 N O6 P 185.072 n PHOSPHOSERINE PHOSPHONOSERINE 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 US Genes Dev. GEDEEP 2056 0890-9369 25 1275 1288 10.1101/gad.2060811 21685363 A Smad action turnover switch operated by WW domain readers of a phosphoserine code. 2011 10.2210/pdb2laj/pdb pdb_00002laj 5210.877 E3 ubiquitin-protein ligase NEDD4-like 6.3.2.- WW 3 domain residues 496-535 1 man polymer 1112.966 Mothers against decapentaplegic homolog 3 sequence database residues 202-211 1 syn polymer NEDD4.2, Nedd4-2 MAD homolog 3, Mad3, Mothers against DPP homolog 3, hMAD-3, JV15-2, SMAD family member 3, SMAD 3, Smad3, hSMAD3 no no GAMEQSFLPPGWEMRIAPNGRPFFYDHNTKTTTWEDPRLKFPVH GAMEQSFLPPGWEMRIAPNGRPFFYDHNTKTTTWEDPRLKFPVH A polypeptide(L) no yes AG(SEP)PNL(SEP)PNP AGSPNLSPNP B 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 human sample NEDD4L, KIAA0439, NEDL3 9606 Homo sapiens 511693 Escherichia coli BL21 petM11 Third WW domain of human Nedd4L (residues 476-515) in complex with doubly phosphorylated human smad3 derived peptide (residues 202-211). database_2 pdbx_database_status pdbx_nmr_software struct_conn struct_ref_seq_dif repository Initial release Version format compliance Data collection Database references Derived calculations Other 1 0 2011-07-06 1 1 2011-07-13 1 2 2023-06-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details BMRB Y RCSB 2011-03-16 REL REL REL REL 9606 human Homo sapiens sample 448 0 237 53 174 structures with acceptable covalent geometry 300 15 2D 1H-1H NOESY 2D 1H-1H TOCSY 3D CBCA(CO)NH 3D HNCACB 2D 1H-15N HSQC 1 mM 3 mM 20 mM 100 mM 2 mM 1 mM [U-100% 15N] 3 mM 20 mM 100 mM 2 mM 1 mM [U-100% 13C; U-100% 15N] 3 mM 20 mM 100 mM 2 mM 0.420 7 ambient 285 K simulated annealing 1 lowest energy 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O 90% H2O/10% D2O 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O 90% H2O/10% D2O 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O 90% H2O/10% D2O Brunger, Adams, Clore, Gros, Nilges and Read structure solution CNS 1.3 Bartels et al. chemical shift assignment XEASY Bruker Biospin collection TopSpin Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Brunger, Adams, Clore, Gros, Nilges and Read refinement CNS 1.3 600 Bruker DRX Bruker DRX n 1 472 A n 2 473 A n 3 474 A n 4 475 A GLN 476 n 5 GLN 476 A SER 477 n 6 SER 477 A PHE 478 n 7 PHE 478 A LEU 479 n 8 LEU 479 A PRO 480 n 9 PRO 480 A PRO 481 n 10 PRO 481 A GLY 482 n 11 GLY 482 A TRP 483 n 12 TRP 483 A GLU 484 n 13 GLU 484 A MET 485 n 14 MET 485 A ARG 486 n 15 ARG 486 A ILE 487 n 16 ILE 487 A ALA 488 n 17 ALA 488 A PRO 489 n 18 PRO 489 A ASN 490 n 19 ASN 490 A GLY 491 n 20 GLY 491 A ARG 492 n 21 ARG 492 A PRO 493 n 22 PRO 493 A PHE 494 n 23 PHE 494 A PHE 495 n 24 PHE 495 A TYR 496 n 25 TYR 496 A ASP 497 n 26 ASP 497 A HIS 498 n 27 HIS 498 A ASN 499 n 28 ASN 499 A THR 500 n 29 THR 500 A LYS 501 n 30 LYS 501 A THR 502 n 31 THR 502 A THR 503 n 32 THR 503 A THR 504 n 33 THR 504 A TRP 505 n 34 TRP 505 A GLU 506 n 35 GLU 506 A ASP 507 n 36 ASP 507 A PRO 508 n 37 PRO 508 A ARG 509 n 38 ARG 509 A LEU 510 n 39 LEU 510 A LYS 511 n 40 LYS 511 A PHE 512 n 41 PHE 512 A PRO 513 n 42 PRO 513 A VAL 514 n 43 VAL 514 A HIS 515 n 44 HIS 515 A ALA 202 n 1 ALA 202 B GLY 203 n 2 GLY 203 B SEP 204 n 3 SEP 204 B PRO 205 n 4 PRO 205 B ASN 206 n 5 ASN 206 B LEU 207 n 6 LEU 207 B SEP 208 n 7 SEP 208 B PRO 209 n 8 PRO 209 B ASN 210 n 9 ASN 210 B PRO 211 n 10 PRO 211 B author_defined_assembly 2 dimeric B SEP 204 PHOSPHOSERINE B SEP 3 SER B SEP 208 PHOSPHOSERINE B SEP 7 SER 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 N ALA 488 A N ALA 17 A O ARG 492 A O ARG 21 A N PHE 495 A N PHE 24 A O THR 504 A O THR 33 1 A GLY 472 A GLY 1 1 Y 1 A ALA 473 A ALA 2 1 Y 1 A MET 474 A MET 3 1 Y 1 A GLU 475 A GLU 4 1 Y 2 A GLY 472 A GLY 1 1 Y 2 A ALA 473 A ALA 2 1 Y 2 A MET 474 A MET 3 1 Y 2 A GLU 475 A GLU 4 1 Y 3 A GLY 472 A GLY 1 1 Y 3 A ALA 473 A ALA 2 1 Y 3 A MET 474 A MET 3 1 Y 3 A GLU 475 A GLU 4 1 Y 4 A GLY 472 A GLY 1 1 Y 4 A ALA 473 A ALA 2 1 Y 4 A MET 474 A MET 3 1 Y 4 A GLU 475 A GLU 4 1 Y 5 A GLY 472 A GLY 1 1 Y 5 A ALA 473 A ALA 2 1 Y 5 A MET 474 A MET 3 1 Y 5 A GLU 475 A GLU 4 1 Y 6 A GLY 472 A GLY 1 1 Y 6 A ALA 473 A ALA 2 1 Y 6 A MET 474 A MET 3 1 Y 6 A GLU 475 A GLU 4 1 Y 7 A GLY 472 A GLY 1 1 Y 7 A ALA 473 A ALA 2 1 Y 7 A MET 474 A MET 3 1 Y 7 A GLU 475 A GLU 4 1 Y 8 A GLY 472 A GLY 1 1 Y 8 A ALA 473 A ALA 2 1 Y 8 A MET 474 A MET 3 1 Y 8 A GLU 475 A GLU 4 1 Y 9 A GLY 472 A GLY 1 1 Y 9 A ALA 473 A ALA 2 1 Y 9 A MET 474 A MET 3 1 Y 9 A GLU 475 A GLU 4 1 Y 10 A GLY 472 A GLY 1 1 Y 10 A ALA 473 A ALA 2 1 Y 10 A MET 474 A MET 3 1 Y 10 A GLU 475 A GLU 4 1 Y 11 A GLY 472 A GLY 1 1 Y 11 A ALA 473 A ALA 2 1 Y 11 A MET 474 A MET 3 1 Y 11 A GLU 475 A GLU 4 1 Y 12 A GLY 472 A GLY 1 1 Y 12 A ALA 473 A ALA 2 1 Y 12 A MET 474 A MET 3 1 Y 12 A GLU 475 A GLU 4 1 Y 13 A GLY 472 A GLY 1 1 Y 13 A ALA 473 A ALA 2 1 Y 13 A MET 474 A MET 3 1 Y 13 A GLU 475 A GLU 4 1 Y 14 A GLY 472 A GLY 1 1 Y 14 A ALA 473 A ALA 2 1 Y 14 A MET 474 A MET 3 1 Y 14 A GLU 475 A GLU 4 1 Y 15 A GLY 472 A GLY 1 1 Y 15 A ALA 473 A ALA 2 1 Y 15 A MET 474 A MET 3 1 Y 15 A GLU 475 A GLU 4 1 Y 1 A A HD11 HG2 LEU PRO 479 508 1.30 2 B B H3 O3P ALA SEP 202 204 1.56 3 A A HG3 HE1 PRO PHE 480 512 1.34 3 B B H2 O1P ALA SEP 202 204 1.56 4 A A HD11 HG2 LEU PRO 479 508 1.31 5 A A HG3 HE1 PRO PHE 480 512 1.23 5 A A HZ2 HZ3 TRP LYS 483 511 1.23 5 B B H3 O3P ALA SEP 202 204 1.60 8 A A HG3 HE1 PRO PHE 480 512 1.19 8 A B HD22 O1P ASN SEP 490 208 1.55 9 A A HD13 HG2 LEU PRO 479 508 1.30 9 A A HE3 HG12 LYS VAL 511 514 1.32 9 A A HE2 HB2 PHE MET 478 485 1.33 10 A A HG3 HE1 PRO PHE 480 512 1.19 11 A A HG3 HE1 PRO PHE 480 512 1.10 11 A A OD1 HZ3 ASP LYS 497 511 1.59 12 A B HD22 O1P ASN SEP 490 208 1.50 12 B B H2 O1P ALA SEP 202 204 1.58 14 A B HG1 HG3 THR PRO 503 209 1.20 15 A A HB2 HB3 GLN LEU 476 479 1.23 1 A A PHE LEU 478 479 -132.73 1 A A GLY TRP 482 483 -141.84 2 A A PHE LEU 478 479 -134.07 2 A A GLY TRP 482 483 -138.68 3 A A PHE LEU 478 479 -131.71 3 A A GLY TRP 482 483 -143.28 4 A A PHE LEU 478 479 -132.27 4 A A GLY TRP 482 483 -142.03 5 A A PHE LEU 478 479 -131.29 5 A A GLY TRP 482 483 -141.46 6 A A PHE LEU 478 479 -130.29 6 A A GLY TRP 482 483 -140.10 7 A A PHE LEU 478 479 -133.21 7 A A GLY TRP 482 483 -142.54 8 A A PHE LEU 478 479 -130.67 8 A A GLY TRP 482 483 -141.96 9 A A PHE LEU 478 479 -129.79 9 A A GLY TRP 482 483 -142.35 10 A A PHE LEU 478 479 -130.01 10 A A GLY TRP 482 483 -141.88 11 A A PHE LEU 478 479 -130.78 11 A A GLY TRP 482 483 -141.90 12 A A PHE LEU 478 479 -131.45 12 A A GLY TRP 482 483 -141.61 13 A A PHE LEU 478 479 -130.39 13 A A GLY TRP 482 483 -141.03 14 A A PHE LEU 478 479 -131.70 14 A A GLY TRP 482 483 -141.74 15 A A PHE LEU 478 479 -134.57 15 A A GLY TRP 482 483 -144.88 1 -16.66 2.00 110.40 93.74 A A A CB CA C PHE PHE PHE 478 478 478 N 1 -5.12 0.70 120.80 115.68 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 2 -13.33 2.00 110.40 97.07 A A A CB CA C PHE PHE PHE 478 478 478 N 3 -14.62 2.00 110.40 95.78 A A A CB CA C PHE PHE PHE 478 478 478 N 3 -5.60 0.70 120.80 115.20 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 4 -14.90 2.00 110.40 95.50 A A A CB CA C PHE PHE PHE 478 478 478 N 4 -5.15 0.70 120.80 115.65 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 5 -14.80 2.00 110.40 95.60 A A A CB CA C PHE PHE PHE 478 478 478 N 5 -5.81 0.70 120.80 114.99 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 6 -12.88 2.00 110.40 97.52 A A A CB CA C PHE PHE PHE 478 478 478 N 6 -4.92 0.70 120.80 115.88 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 7 -16.53 2.00 110.40 93.87 A A A CB CA C PHE PHE PHE 478 478 478 N 7 -4.41 0.70 120.80 116.39 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 8 -13.81 2.00 110.40 96.59 A A A CB CA C PHE PHE PHE 478 478 478 N 8 -6.06 0.70 120.80 114.74 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 9 -13.98 2.00 110.40 96.42 A A A CB CA C PHE PHE PHE 478 478 478 N 9 -5.91 0.70 120.80 114.89 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 9 9.32 1.50 119.30 128.62 A A A C N CA PHE PRO PRO 512 513 513 Y 10 -14.63 2.00 110.40 95.77 A A A CB CA C PHE PHE PHE 478 478 478 N 11 -14.18 2.00 110.40 96.22 A A A CB CA C PHE PHE PHE 478 478 478 N 11 -6.04 0.70 120.80 114.76 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 12 -15.66 2.00 110.40 94.74 A A A CB CA C PHE PHE PHE 478 478 478 N 12 -5.40 0.70 120.80 115.40 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 12 4.39 0.70 120.80 125.19 A A A CB CG CD1 PHE PHE PHE 494 494 494 N 13 -14.44 2.00 110.40 95.96 A A A CB CA C PHE PHE PHE 478 478 478 N 13 -4.52 0.70 120.80 116.28 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 14 -15.11 2.00 110.40 95.29 A A A CB CA C PHE PHE PHE 478 478 478 N 14 -5.35 0.70 120.80 115.45 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 15 -14.52 2.00 110.40 95.88 A A A CB CA C PHE PHE PHE 478 478 478 N 15 -5.40 0.70 120.80 115.40 A A A CB CG CD2 PHE PHE PHE 478 478 478 N 1 A PRO 480 -59.89 174.05 1 A PRO 481 -79.30 38.30 1 A PRO 489 -56.36 1.86 1 A PRO 513 -48.96 -9.63 1 B PRO 205 -59.62 100.03 1 B LEU 207 -63.21 99.24 2 A PRO 481 -88.59 30.16 2 A PRO 489 -54.38 2.78 2 A PRO 513 -48.73 -9.51 2 A VAL 514 -58.22 -9.67 2 B PRO 205 -59.53 98.22 3 A PRO 481 -79.52 29.15 3 A PRO 489 -55.95 0.94 3 A PRO 513 -50.86 -9.70 3 B PRO 205 -59.68 98.48 4 A PRO 480 -59.82 173.96 4 A PRO 481 -78.22 36.00 4 A PRO 489 -54.96 -3.78 4 A PHE 512 -39.63 -39.69 4 A PRO 513 -49.63 -9.61 4 A VAL 514 -57.47 -9.50 4 B PRO 205 -59.58 106.24 5 A PRO 480 -59.78 171.54 5 A PRO 481 -74.79 28.83 5 A PRO 489 -57.67 -2.19 5 A PRO 513 -50.40 -9.85 5 A VAL 514 -59.96 -9.61 6 A SER 477 -120.15 -75.24 6 A PRO 481 -80.17 34.86 6 A PRO 489 -52.68 -4.11 6 A PRO 513 -48.06 -9.42 6 A VAL 514 -57.35 -9.86 6 B PRO 205 -59.63 106.25 6 B LEU 207 -61.47 99.89 7 A PRO 481 -78.12 36.74 7 A PRO 489 -57.83 5.44 7 A ASN 499 -164.60 -74.43 7 A PHE 512 -39.96 -32.08 7 A PRO 513 -46.95 -8.90 7 A VAL 514 -46.43 -9.86 7 B PRO 205 -59.65 105.68 8 A PRO 480 -59.80 171.82 8 A PRO 481 -77.51 24.48 8 A PRO 489 -57.61 -4.16 8 A PHE 512 -39.67 -39.31 8 A PRO 513 -50.98 -9.62 8 B PRO 205 -59.62 102.76 9 A PRO 480 -59.91 174.38 9 A PRO 481 -74.43 24.62 9 A PRO 489 -52.78 -3.19 9 A PRO 513 -42.81 -8.92 9 A VAL 514 -45.39 -9.74 9 B PRO 205 -59.60 106.09 10 A PRO 480 -59.86 170.65 10 A PRO 481 -77.09 35.07 10 A PRO 489 -58.82 5.73 10 B PRO 205 -59.98 105.70 11 A SER 477 -96.92 -75.25 11 A PRO 480 -59.95 175.28 11 A PRO 481 -79.22 30.68 11 A PRO 489 -59.70 3.20 11 B PRO 205 -59.41 100.39 12 A PRO 481 -78.74 34.61 12 A PRO 489 -56.90 1.79 12 A PRO 513 -46.63 -9.70 12 B PRO 205 -59.67 109.68 13 A PRO 489 -54.55 -4.57 13 A PHE 512 -39.36 -33.58 13 A PRO 513 -43.76 -9.13 13 A VAL 514 -48.02 -9.82 14 A PRO 481 -79.23 36.02 14 A PRO 489 -58.00 4.28 14 A PHE 512 -39.33 -35.76 14 A PRO 513 -42.51 -8.88 14 A VAL 514 -41.45 -9.73 14 B PRO 205 -59.54 98.83 15 A PRO 480 -59.93 172.65 15 A PRO 481 -74.42 29.16 15 A PRO 489 -54.41 -2.51 15 A PHE 512 -39.65 -38.11 15 A PRO 513 -45.87 -9.84 15 B PRO 205 -59.86 108.04 N lowest energy, model 1 Third WW domain of human Nedd4L in complex with doubly phosphorylated human smad3 derived peptide 1 N N 2 N N A ASP 507 A ASP 36 HELX_P A HIS 515 A HIS 44 5 1 9 covale 1.318 both B GLY 203 B C GLY 2 1_555 B SEP 204 B N SEP 3 1_555 covale 1.336 both B SEP 204 B C SEP 3 1_555 B PRO 205 B N PRO 4 1_555 covale 1.325 both B LEU 207 B C LEU 6 1_555 B SEP 208 B N SEP 7 1_555 covale 1.344 both B SEP 208 B C SEP 7 1_555 B PRO 209 B N PRO 8 1_555 LIGASE/TRANSCRIPTION REGULATOR CDK, signal transduction, LIGASE-TRANSCRIPTION REGULATOR complex NED4L_HUMAN UNP 1 496 Q96PU5 QSFLPPGWEMRIAPNGRPFFIDHNTKTTTWEDPRLKFPVH SMAD3_HUMAN UNP 2 202 P84022 AGSPNLSPNP 496 535 2LAJ 476 515 Q96PU5 A 1 5 44 202 211 2LAJ 202 211 P84022 B 2 1 10 1 expression tag GLY 472 2LAJ A Q96PU5 UNP 1 1 expression tag ALA 473 2LAJ A Q96PU5 UNP 2 1 expression tag MET 474 2LAJ A Q96PU5 UNP 3 1 expression tag GLU 475 2LAJ A Q96PU5 UNP 4 1 ILE engineered mutation TYR 496 2LAJ A Q96PU5 UNP 516 25 3 anti-parallel anti-parallel A TRP 483 A TRP 12 A ALA 488 A ALA 17 A ARG 492 A ARG 21 A ASP 497 A ASP 26 A THR 502 A THR 31 A THR 504 A THR 33