Entry | Database: PDB / ID: 2jaw |
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Title | Crystal structure of D41N variant of human mitochondrial 5'(3')- deoxyribonucleotidase (mdN) in complex with 5-bromovinyldeoxyuridine 5'-monophosphate |
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Components | 5'(3')-DEOXYRIBONUCLEOTIDASE |
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Keywords | HYDROLASE / TRANSIT PEPTIDE / NUCLEOTIDE-BINDING / MITOCHONDRIAL / METAL-BINDING / ALFA BETA FOLD / NUCLEOTIDE- BINDING / NUCLEOTIDE METABOLISM / MAGNESIUM / MITOCHONDRION |
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Function / homology | Function and homology information
pyrimidine deoxyribonucleotide catabolic process / nucleotidase activity / dUMP catabolic process / Pyrimidine catabolism / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / DNA replication / mitochondrial matrix / nucleotide binding / mitochondrion / metal ion bindingSimilarity search - Function 5'(3')-deoxyribonucleotidase / 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) / Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...5'(3')-deoxyribonucleotidase / 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) / Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha BetaSimilarity search - Domain/homology |
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Biological species | HOMO SAPIENS (human) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å |
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Authors | Wallden, K. / Ruzzenente, B. / Bianchi, V. / Nordlund, P. |
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Citation | Journal: Biochemistry / Year: 2007 Title: Crystal Structures of Human and Murine Deoxyribonucleotidases: Insights Into Recognition of Substrates and Nucleotide Analogues. Authors: Wallden, K. / Rinaldo-Matthis, A. / Ruzzenente, B. / Rampazzo, C. / Bianchi, V. / Nordlund, P. |
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History | Deposition | Nov 30, 2006 | Deposition site: PDBE / Processing site: PDBE |
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Revision 1.0 | Nov 20, 2007 | Provider: repository / Type: Initial release |
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Revision 1.1 | May 8, 2011 | Group: Version format compliance |
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Revision 1.2 | Jul 13, 2011 | Group: Version format compliance |
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Revision 1.3 | Jan 30, 2019 | Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval |
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Revision 1.4 | Feb 6, 2019 | Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp |
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Revision 1.5 | Jul 10, 2019 | Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site |
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Revision 1.6 | Jul 24, 2019 | Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site |
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Revision 1.7 | May 8, 2024 | Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id |
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