5IW4
Crystal structure of E. coli NudC in complex with NAD
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000210 | molecular_function | NAD+ diphosphatase activity |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0006402 | biological_process | mRNA catabolic process |
| A | 0006742 | biological_process | NADP+ catabolic process |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0019677 | biological_process | NAD+ catabolic process |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0035529 | molecular_function | NADH pyrophosphatase activity |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0048255 | biological_process | mRNA stabilization |
| A | 0110153 | molecular_function | RNA NAD-cap (NMN-forming) hydrolase activity |
| A | 0110155 | biological_process | NAD-cap decapping |
| B | 0000210 | molecular_function | NAD+ diphosphatase activity |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0006402 | biological_process | mRNA catabolic process |
| B | 0006742 | biological_process | NADP+ catabolic process |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0019677 | biological_process | NAD+ catabolic process |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0035529 | molecular_function | NADH pyrophosphatase activity |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0048255 | biological_process | mRNA stabilization |
| B | 0110153 | molecular_function | RNA NAD-cap (NMN-forming) hydrolase activity |
| B | 0110155 | biological_process | NAD-cap decapping |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 500 |
| Chain | Residue |
| A | CYS98 |
| A | CYS101 |
| A | CYS116 |
| A | CYS119 |
| site_id | AC2 |
| Number of Residues | 15 |
| Details | binding site for residue NAD A 501 |
| Chain | Residue |
| A | SER199 |
| A | MET201 |
| A | THR239 |
| A | VAL240 |
| A | ALA241 |
| A | HOH602 |
| A | HOH629 |
| B | LYS25 |
| B | GLU111 |
| B | TYR124 |
| A | ALA128 |
| A | PHE160 |
| A | GLN192 |
| A | TRP194 |
| A | PHE196 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 500 |
| Chain | Residue |
| B | CYS98 |
| B | CYS101 |
| B | CYS116 |
| B | CYS119 |
| site_id | AC4 |
| Number of Residues | 11 |
| Details | binding site for residue NAD B 501 |
| Chain | Residue |
| A | TYR124 |
| A | HOH626 |
| B | ALA128 |
| B | CYS130 |
| B | PHE160 |
| B | TRP194 |
| B | PHE196 |
| B | MET201 |
| B | THR239 |
| B | VAL240 |
| B | ALA241 |
Functional Information from PROSITE/UniProt
| site_id | PS00893 |
| Number of Residues | 22 |
| Details | NUDIX_BOX Nudix box signature. GfvevgEtleqAVaREVmEEsG |
| Chain | Residue | Details |
| A | GLY159-GLY180 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 246 |
| Details | Domain: {"description":"Nudix hydrolase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00794","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 42 |
| Details | Motif: {"description":"Nudix box","evidences":[{"source":"PROSITE-ProRule","id":"PRU00794","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"27428510","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5IW4","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"27428510","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5IW5","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"27428510","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27561816","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli K12 at 2.20 A resolution.","authoringGroup":["Joint center for structural genomics (JCSG)"]}},{"source":"PDB","id":"1VK6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GB5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5ISY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5IW4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5IW5","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"27561816","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5ISY","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 18 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"27428510","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27561816","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5ISY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5IW4","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"Q9DCN1","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
