The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.
Total Genus |
146
|
sequence length |
433
|
structure length |
433
|
Chain Sequence |
MRMVDIIIKKQNGKELTTEEIQFFVNGYTDGSIPDYQASALAMAIFFRDMSDRERADLTMAMVNSGETIDLSAIEGIKVDKHSTGGVGDTTTLVLAPLVAALDVPVAKMSGRGLGHTGGTIDKLEAIDGFHVELTKREFIKLVNRDKVAVIGQSGNLTPADKKLYALRDVTGTVNSIPLIASSIMSKKIAAGADAIVLDVKTGAGAFMKTEEDAAELAKAMVRIGNNVGRQTMAVISDMSQPLGFAIGNALEVKEAIDTLKGEGPEDLHELVLTLGSQMVVLAKKADTLDEARAKLEEVMKNGKALEKFKDFLKNQGGDSSIVDDPSKLPQAAYQIDVPAKEAGVVSEIVADEIGVAAMLLGAGRATKEDEIDLAVGIMLRKKVGDKVEKGEPLVTLYANRENVDEVIAKVYDNIRIAAEAKAPKLIHTLITE
|
The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.
After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.
| publication title |
X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis with Sulfate Ion
rcsb |
| molecule tags |
Transferase
|
| source organism |
Bacillus subtilis subsp. subtilis str. 168
|
| molecule keywords |
Pyrimidine-nucleoside phosphorylase
|
| total genus |
146
|
| structure length |
433
|
| sequence length |
433
|
| chains with identical sequence |
B
|
| ec nomenclature |
ec
2.4.2.2: Pyrimidine-nucleoside phosphorylase. |
| pdb deposition date | 2015-11-11 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF00591 | Glycos_transf_3 | Glycosyl transferase family, a/b domain |
| A | PF02885 | Glycos_trans_3N | Glycosyl transferase family, helical bundle domain |
| A | PF07831 | PYNP_C | Pyrimidine nucleoside phosphorylase C-terminal domain |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Mainly Alpha | Up-down Bundle | Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 | Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C | ||
| Alpha Beta | 3-Layer(aba) Sandwich | Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | ||
| Alpha Beta | Alpha-Beta Complex | Aldehyde Oxidoreductase; domain 3 | Pyrimidine nucleoside phosphorylase-like, C-terminal domain |
#chains in the Genus database with same CATH superfamily 3R6C A; 4M0R A; 4GA4 A; 2DSJ A; 4YEK A; 4XR5 A; 4GTN A; 1ZYK A; 4ZTV A; 1GXB A; 4YI7 A; 2BPQ A; 1VQU A; 4GKM A; 5BO2 A; 4OWO A; 4OWV A; 4EAD A; 5C7S A; 4X5E A; 3UU1 A; 1ZVW A; 2ELC A; 3R88 A; 1KGZ A; 3GBR A; 2GVQ A; 3QR9 A; 1AZY A; 1V8G A; 3QS8 A; 3QQS A; 4X46 A; 4N5V A; 4N8Q A; 4ZOF A; 1OTP A; 2J0F A; 4OWM A; 4N93 A; 3H5Q A; 2WK6 A; 4OWQ A; 4YYY A; 4GA6 A; 1O17 A; 4ZOK A; 4MUO A; 2WK5 A; 4X5D A; 5C2L A; 1BRW A; 5BO3 A; 4EAF A; 4OWS A; 4IJ1 A; 1ZXY A; 5EP8 A; 4GIU A; 4X58 A; 3TWP A; 4LHM A; 1UOU A; 4X5C A; 5C1R A; 4OWN A; 1KHD A; 4X5B A; 5EY3 A; 2TPT A; 4X5A A; 3QSA A; 5BNE A; 4HKM A; 5BYT A; 4OWU A; 4GA5 A; 4X59 A; 4ZOJ A; #chains in the Genus database with same CATH topology 1FFV B; 1N61 B; 1FIQ C; 3AMZ A; 2E3T A; 3R6C A; 4M0R A; 4GA4 A; 2I14 A; 1FO4 A; 2DSJ A; 1M1K J; 5HUO A; 4YEK A; 4XR5 A; 4GTN A; 3BII E; 3G4S H; 1ZYK A; 2B7Q A; 4ZTV A; 1GXB A; 1YTD A; 4YI7 A; 1YIT H; 1N62 B; 2B7P A; 2BPQ A; 1VQ9 H; 1YIJ H; 5JVH J; 1VQU A; 3WO0 A; 5AYY A; 4WF9 J; 3C2R A; 3L4P A; 4GKM A; 3CC2 H; 5BO2 A; 1KC8 J; 5HL7 J; 1VQ8 H; 4OWO A; 4OWV A; 4EAD A; 5C7S A; 3NRZ C; 1QVG H; 4X5E A; 3UU1 A; 1ZVW A; 1JRO B; 1ZXI B; 2ELC A; 3R88 A; 3CCR H; 4WFN J; 1VQN H; 3NS1 C; 2QEX H; 2OTJ H; 3CC4 H; 2ZJQ J; 1KGZ A; 3GBR A; 1X1O A; 4U67 J; 3L0G A; 1Q82 J; 2W3S B; 2GVQ A; 3NVW C; 3QR9 A; 5AYX A; 1N8R J; 3NVY C; 3OW2 H; 1AZY A; 1V8G A; 2PA2 A; 1Q7Y J; 5MLC O; 3QS8 A; 1YJN H; 3QQS A; 4X46 A; 3I55 H; 3TQV A; 5HUP A; 4N5V A; 4N8Q A; 4ZOF A; 1N5W B; 5MPO C; 1OTP A; 1YJW H; 3C2E A; 2J0F A; 3I56 H; 1YHQ H; 4OWM A; 1VDV A; 1YTE A; 1RM6 A; 4IOA J; 1KD1 J; 5JVG J; 1QPN A; 3AM9 A; 4N93 A; 3WO1 A; 5AN9 F; 2ZJP J; 1N63 B; 3H5Q A; 4C80 A; 1WKI A; 5DM7 J; 1QAP A; 2JBM A; 1FFU B; 2WK6 A; 4I9A A; 5GAG N; 4OWQ A; 4YYY A; 1N60 B; 3PIP J; 1QVF H; 4GA6 A; 1QPQ A; 3CPW H; 3CCU H; 1O17 A; 1FM0 E; 2W3R B; 4ZOK A; 5AYZ A; 4C7Y A; 1YJ9 H; 3C2V A; 4IOC J; 1KQS H; 3CME H; 3CD6 H; 4WFA J; 1VQ6 H; 4MUO A; 3CCM H; 2WK5 A; 1S72 H; 4X5D A; 1VQ4 H; 5C2L A; 1BRW A; 5H1S O; 5BO3 A; 4F3F C; 1VLB A; 4AP8 A; 3NVZ C; 4EAF A; 3PIO J; 1VQK H; 1NJI J; 1K9M J; 1Q86 J; 4OWS A; 3J7Z M; 1W2B H; 2QIE A; 4ZOH A; 2W55 B; 3FAH A; 3CCV H; 4IJ1 A; 1YTK A; 3ETR C; 3CCJ H; 2OMD A; 1ZXY A; 4KWV A; 5GAE N; 1VQP H; 5EP8 A; 1QPO A; 3AN1 A; 1DGJ A; 3NVV C; 3PAJ A; 4GIU A; 4X58 A; 3B9J C; 3EUB 4; 3RPF A; 3TWP A; 3SR6 C; 4LHM A; 4WFB J; 1K73 J; 1NVI E; 1UOU A; 1VQO H; 3CCQ H; 3CC7 H; 1SIJ A; 1WYG A; 5GAH N; 4IO9 J; 4X5C A; 1O4U A; 5C1R A; 1V97 A; 3VMM A; 4OWN A; 3G71 H; 3CCE H; 4UY8 M; 1FMA E; 1N5X A; 3CCL H; 2B7N A; 3CCS H; 4KWW A; 4WCE J; 3CMA H; 1RRZ A; 1KHD A; 4US9 A; 4X5B A; 2WP4 A; 3FC4 A; 3C2O A; 2OTL H; 2Q5W E; 4USA A; 1RF8 B; 1K8A J; 1VQ5 H; 3G6E H; 2ZJR J; 3C2F A; 5EY3 A; 1JJ2 H; 4US8 A; 3DLL J; 1VQL H; 2TPT A; 4X5A A; 1VQM H; 3CXC H; 3QSA A; 5BNE A; 1JRP B; 2I1O A; 5HUL A; 1SB3 A; 5DM6 J; 3WNZ A; 4HKM A; 5BYT A; 3GNN A; 1M90 J; 1Q81 J; 4OWU A; 4GA5 A; 1NVJ A; 1QPR A; 3CF5 J; 2QA4 H; 5GAD N; 1YI2 H; 2W54 B; 4C7Z A; 1VQ7 H; 1Y69 K; 4X59 A; 4ZOJ A; #chains in the Genus database with same CATH homology 3R6C A; 4M0R A; 4GA4 A; 2DSJ A; 4YEK A; 4XR5 A; 4GTN A; 1ZYK A; 4ZTV A; 1GXB A; 4YI7 A; 2BPQ A; 1VQU A; 4GKM A; 5BO2 A; 4OWO A; 4OWV A; 4EAD A; 5C7S A; 4X5E A; 3UU1 A; 1ZVW A; 2ELC A; 3R88 A; 1KGZ A; 3GBR A; 2GVQ A; 3QR9 A; 1AZY A; 1V8G A; 3QS8 A; 3QQS A; 4X46 A; 4N5V A; 4N8Q A; 4ZOF A; 1OTP A; 2J0F A; 4OWM A; 4N93 A; 3H5Q A; 2WK6 A; 4OWQ A; 4YYY A; 4GA6 A; 1O17 A; 4ZOK A; 4MUO A; 2WK5 A; 4X5D A; 5C2L A; 1BRW A; 5BO3 A; 4EAF A; 4OWS A; 4IJ1 A; 1ZXY A; 5EP8 A; 4GIU A; 4X58 A; 3TWP A; 4LHM A; 1UOU A; 4X5C A; 5C1R A; 4OWN A; 1KHD A; 4X5B A; 5EY3 A; 2TPT A; 4X5A A; 3QSA A; 5BNE A; 4HKM A; 5BYT A; 4OWU A; 4GA5 A; 4X59 A; 4ZOJ A;
#similar chains in the Genus database (?% sequence similarity) ...loading similar chains, please wait... #similar chains, but unknotted ...loading similar chains, please wait... #similar chains in the pdb database (?% sequence similarity) ...loading similar chains, please wait...
