4B2OA

Crystal structure of bacillus subtilis ymdb, a global regulator of late adaptive responses.
Total Genus 95
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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
95
sequence length
264
structure length
264
Chain Sequence
MRILFIGDVVGSPGRDMVKEYVPKLKTKYKPHFTIINGENAAHGKGLTEKIYHSLIQSGADAITMGNHTWDKKEIFDFIDDVPNLVRPANFPEGTPGKGITYVKANGKELAVINLQGRTFLPPLDDPFLKADELIAEAAKRTPYIFIDFHAEATSEKLALGWYTDGRASAVVGTHTHVQTADNRILPKGTAYITDVGMTGPYDGILGMDRETIIKRFKTNLPVRFTVAEGKTTLSGVVIDIDDQTKKAVKIERILINDDHMFFE
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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.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title The Ymdb Phosphodiesterase is a Global Regulator of Late Adaptive Responses in Bacillus Subtilis.
pubmed doi rcsb
source organism Bacillus subtilis subsp. subtilis
molecule tags Hydrolase
molecule keywords YMDB PHOSPHODIESTERASE
total genus 95
structure length 264
sequence length 264
chains with identical sequence B, C, D
ec nomenclature ec 3.1.4.16: 2',3'-cyclic-nucleotide 2'-phosphodiesterase.
pdb deposition date 2012-07-17

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00149 Metallophos Calcineurin-like phosphoesterase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.60.21.10 Alpha Beta 4-Layer Sandwich Purple Acid Phosphatase; chain A, domain 2 Purple Acid Phosphatase; chain A, domain 2 4b2oA00
2P6BA 3DW8C 4I5NC 4MP0A 4YKEA 4ZX2A 2IE4C 5EQVA 4OR9A 1USHA 1S3MA 3JYFA 4JA7A 3THNA 1Z2XA 1WARA 1S3NA 4UWQA 3QFMA 4FBQA 5JJTA 2WDCA 3H64A 2IAEC 4H2FA 4V0XA 1S3LA 2Z1AA 3QFKA 4O24A 1NNWA 4DT2A 4Q7FA 1Z2WA 5IOHA 4KKZA 5JPEA 4XPNA 1FJMA 3H63A 2O8GA 1KBPA 1T71A 5INBA 3C5WC 2WDEA 5DNYA 2IE3C 4FBWA 1HP1A 1II7A 2HYPA 4H2GA 2BCDA 2QFRA 4O43A 2AHDA 2Z06A 3H68A 2BQ8X 1OI8A 4O5GA 3AV0A 2GJUA 3N5UA 3CK2A 1XZWA 3ZU0A 2JOGA 3QFOA 5C1VA 1MF8A 2Q8UA 4LU9A 3ZTVA 4UT3B 4I5LC 3H62B 4HD0A 3AUZA 1OIDA 3H60A 3QFNA 4KBPA 1W24A 1V73A 4H2BA 4JA9A 5B8IA 3RL4A 3HVQA 3IB7A 3RQZA 4DSYA 3EGGA 4DHLA 4MOYA 3IB8A 3LL8A 3K7VC 1UF3A 2ZBMA 3H61A 1AUIA 1XM7A 2WDFA 4FCXA 1IT6A 4ORCA 4UT2A 2O8AA 4FBKA 4WWLA 2NXFA 2Z72A 3C9FA 2BDXA 3DSDA 3RL3A 3E7AA 4IL1A 4V0VA 5F3WA 3E7BA 5GTUA 3FGAC 1HO5A 2WDDA 4IYPC 2R17A 2A22A 4ZVZA 4J6OA 2CV9A 1UTEA 3ICFA 2HY1A 4H2IA 2QFPA 4NZVA 5JPFA 5J28A 3PSNA 4LACC 4TUGA 4V0WA 2DFJA 1WAO1 4H1SA 4UT3A 2QJCA 1SU1A 2NYLC 4O4KA 3RL5A 3K7WC 4B2OA 1S70A 3DSCA 2USHA 4ORAA 4G9JA 3V4YA 3PSOA 2YVTA 3H69A 3QG5C 1TCOA 2KKNA 2NPPC 1OIEA 4F0ZA 3EGHA 3H66A 1G5BA 4LTYA 4ORBA 3T1IA 1S8EA 3IVEA 3P71C 4MOVA 1S95A 2XMOA 1QFCA 3TGHA 1U32A 1M63A 1QHWA 5HPEA 2NYMC 3H67A 1HPUA 2HYOA 3KBPA 3IVDA 4M0VA 1T70A 4TUIA 1JK7A 3GVEA 3THOB 4H1YP
chains in the Genus database with same CATH superfamily
2ZO9B 2P6BA 3DW8C 4I5NC 4MP0A 4YKEA 4ZX2A 2IE4C 5EQVA 4OR9A 1USHA 1S3MA 3JYFA 4JA7A 3D03A 3THNA 1Z2XA 1WARA 1S3NA 4UWQA 3QFMA 4FBQA 5JJTA 2WDCA 3H64A 2IAEC 4H2FA 4V0XA 1S3LA 2Z1AA 3QFKA 4O24A 1NNWA 4DT2A 4Q7FA 1Z2WA 5IOHA 4KKZA 5JPEA 4XPNA 3FLOA 1FJMA 3H63A 2O8GA 1KBPA 1T71A 5INBA 3C5WC 2WDEA 5DNYA 2IE3C 4FBWA 1HP1A 1II7A 2HYPA 4H2GA 2BCDA 2QFRA 4O43A 2AHDA 2Z06A 3H68A 2BQ8X 1OI8A 4O5GA 3AV0A 2GJUA 3E0JA 3CK2A 1XZWA 3N5UA 3ZU0A 2JOGA 3QFOA 2ZOAA 5C1VA 2DXLA 1MF8A 2Q8UA 4LU9A 3ZTVA 4UT3B 4I5LC 3H62B 4HD0A 3AUZA 1OIDA 3H60A 3QFNA 4KBPA 1W24A 1V73A 4H2BA 4JA9A 5B8IA 3RL4A 3HVQA 3IB7A 3RQZA 4DSYA 3EGGA 4DHLA 4MOYA 3IB8A 3LL8A 3K7VC 1UF3A 2ZBMA 3H61A 1AUIA 1XM7A 2WDFA 4FCXA 1IT6A 4ORCA 4UT2A 2O8AA 4FBKA 4WWLA 2NXFA 2Z72A 3C9FA 2BDXA 3DSDA 3RL3A 3E7AA 4IL1A 4V0VA 5F3WA 3E7BA 5GTUA 3FGAC 1HO5A 2WDDA 4IYPC 2R17A 2A22A 4ZVZA 4J6OA 2CV9A 1UTEA 3ICFA 2HY1A 4H2IA 2QFPA 4NZVA 5JPFA 5J28A 3PSNA 4LACC 4TUGA 4V0WA 2DFJA 1WAO1 4H1SA 4UT3A 2QJCA 1SU1A 2NYLC 4O4KA 3RL5A 3K7WC 4B2OA 1S70A 3DSCA 2USHA 4ORAA 4G9JA 3V4YA 3PSOA 2YVTA 3H69A 3QG5C 1TCOA 2KKNA 2NPPC 1OIEA 4F0ZA 3EGHA 3H66A 1G5BA 4LTYA 4ORBA 3T1IA 1S8EA 3IVEA 3P71C 4MOVA 1S95A 2YEQA 2XMOA 1QFCA 3TGHA 1U32A 1M63A 1QHWA 5HPEA 2NYMC 3H67A 1HPUA 2HYOA 3KBPA 3IVDA 4M0VA 1T70A 4TUIA 1JK7A 2DXNA 3GVEA 3THOB 4H1YP
chains in the Genus database with same CATH topology
2ZO9B 2P6BA 3DW8C 4I5NC 4MP0A 4YKEA 4ZX2A 2IE4C 5EQVA 4OR9A 1USHA 1S3MA 3JYFA 4JA7A 3D03A 3THNA 1Z2XA 1WARA 1S3NA 4UWQA 3QFMA 4FBQA 5JJTA 2WDCA 3H64A 2IAEC 4H2FA 4V0XA 1S3LA 2Z1AA 3QFKA 4O24A 1NNWA 4DT2A 4Q7FA 1Z2WA 5IOHA 4KKZA 5JPEA 4XPNA 3FLOA 1FJMA 3H63A 2O8GA 1KBPA 1T71A 5INBA 3C5WC 2WDEA 5DNYA 2IE3C 4FBWA 1HP1A 1II7A 2HYPA 4H2GA 2BCDA 2QFRA 4O43A 2AHDA 2Z06A 3H68A 2BQ8X 1OI8A 4O5GA 3AV0A 2GJUA 3E0JA 3CK2A 1XZWA 3N5UA 3ZU0A 2JOGA 3QFOA 2ZOAA 5C1VA 2DXLA 1MF8A 2Q8UA 4LU9A 3ZTVA 4UT3B 4I5LC 3H62B 4HD0A 3AUZA 1OIDA 3H60A 3QFNA 4KBPA 1W24A 1V73A 4H2BA 4JA9A 5B8IA 3RL4A 3HVQA 3IB7A 3RQZA 4DSYA 3EGGA 4DHLA 4MOYA 3IB8A 3LL8A 3K7VC 1UF3A 2ZBMA 3H61A 1AUIA 1XM7A 2WDFA 4FCXA 1IT6A 4ORCA 4UT2A 2O8AA 4FBKA 4WWLA 2NXFA 2Z72A 3C9FA 2BDXA 3DSDA 3RL3A 3E7AA 4IL1A 4V0VA 5F3WA 3E7BA 5GTUA 3FGAC 1HO5A 2WDDA 4IYPC 2R17A 2A22A 4ZVZA 4J6OA 2CV9A 1UTEA 3ICFA 2HY1A 4H2IA 2QFPA 4NZVA 5JPFA 5J28A 3PSNA 4LACC 4TUGA 4V0WA 2DFJA 1WAO1 4H1SA 4UT3A 2QJCA 1SU1A 2NYLC 4O4KA 3RL5A 3K7WC 4B2OA 1S70A 3DSCA 2USHA 4ORAA 4G9JA 3V4YA 3PSOA 2YVTA 3H69A 3QG5C 1TCOA 2KKNA 2NPPC 1OIEA 4F0ZA 3EGHA 3H66A 1G5BA 4LTYA 4ORBA 3T1IA 1S8EA 3IVEA 3P71C 4MOVA 1S95A 2YEQA 2XMOA 1QFCA 3TGHA 1U32A 1M63A 1QHWA 5HPEA 2NYMC 3H67A 1HPUA 2HYOA 3KBPA 3IVDA 4M0VA 1T70A 4TUIA 1JK7A 2DXNA 3GVEA 3THOB 4H1YP
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2P6B A;  3DW8 C;  4I5N C;  4MP0 A;  4YKE A;  4ZX2 A;  2IE4 C;  5EQV A;  4OR9 A;  1USH A;  1S3M A;  3JYF A;  4JA7 A;  3THN A;  1Z2X A;  1WAR A;  1S3N A;  4UWQ A;  3QFM A;  4FBQ A;  5JJT A;  2WDC A;  3H64 A;  2IAE C;  4H2F A;  4V0X A;  1S3L A;  2Z1A A;  3QFK A;  4O24 A;  1NNW A;  4DT2 A;  4Q7F A;  1Z2W A;  5IOH A;  4KKZ A;  5JPE A;  4XPN A;  1FJM A;  3H63 A;  2O8G A;  1KBP A;  1T71 A;  5INB A;  3C5W C;  2WDE A;  5DNY A;  2IE3 C;  4FBW A;  1HP1 A;  1II7 A;  2HYP A;  4H2G A;  2BCD A;  2QFR A;  4O43 A;  2AHD A;  2Z06 A;  3H68 A;  2BQ8 X;  1OI8 A;  4O5G A;  3AV0 A;  2GJU A;  3N5U A;  3CK2 A;  1XZW A;  3ZU0 A;  2JOG A;  3QFO A;  5C1V A;  1MF8 A;  2Q8U A;  4LU9 A;  3ZTV A;  4UT3 B;  4I5L C;  3H62 B;  4HD0 A;  3AUZ A;  1OID A;  3H60 A;  3QFN A;  4KBP A;  1W24 A;  1V73 A;  4H2B A;  4JA9 A;  5B8I A;  3RL4 A;  3HVQ A;  3IB7 A;  3RQZ A;  4DSY A;  3EGG A;  4DHL A;  4MOY A;  3IB8 A;  3LL8 A;  3K7V C;  1UF3 A;  2ZBM A;  3H61 A;  1AUI A;  1XM7 A;  2WDF A;  4FCX A;  1IT6 A;  4ORC A;  4UT2 A;  2O8A A;  4FBK A;  4WWL A;  2NXF A;  2Z72 A;  3C9F A;  2BDX A;  3DSD A;  3RL3 A;  3E7A A;  4IL1 A;  4V0V A;  5F3W A;  3E7B A;  5GTU A;  3FGA C;  1HO5 A;  2WDD A;  4IYP C;  2R17 A;  2A22 A;  4ZVZ A;  4J6O A;  2CV9 A;  1UTE A;  3ICF A;  2HY1 A;  4H2I A;  2QFP A;  4NZV A;  5JPF A;  5J28 A;  3PSN A;  4LAC C;  4TUG A;  4V0W A;  2DFJ A;  1WAO 1;  4H1S A;  4UT3 A;  2QJC A;  1SU1 A;  2NYL C;  4O4K A;  3RL5 A;  3K7W C;  4B2O A;  1S70 A;  3DSC A;  2USH A;  4ORA A;  4G9J A;  3V4Y A;  3PSO A;  2YVT A;  3H69 A;  3QG5 C;  1TCO A;  2KKN A;  2NPP C;  1OIE A;  4F0Z A;  3EGH A;  3H66 A;  1G5B A;  4LTY A;  4ORB A;  3T1I A;  1S8E A;  3IVE A;  3P71 C;  4MOV A;  1S95 A;  2XMO A;  1QFC A;  3TGH A;  1U32 A;  1M63 A;  1QHW A;  5HPE A;  2NYM C;  3H67 A;  1HPU A;  2HYO A;  3KBP A;  3IVD A;  4M0V A;  1T70 A;  4TUI A;  1JK7 A;  3GVE A;  3THO B;  4H1Y P; 
#chains in the Genus database with same CATH topology
 2ZO9 B;  2P6B A;  3DW8 C;  4I5N C;  4MP0 A;  4YKE A;  4ZX2 A;  2IE4 C;  5EQV A;  4OR9 A;  1USH A;  1S3M A;  3JYF A;  4JA7 A;  3D03 A;  3THN A;  1Z2X A;  1WAR A;  1S3N A;  4UWQ A;  3QFM A;  4FBQ A;  5JJT A;  2WDC A;  3H64 A;  2IAE C;  4H2F A;  4V0X A;  1S3L A;  2Z1A A;  3QFK A;  4O24 A;  1NNW A;  4DT2 A;  4Q7F A;  1Z2W A;  5IOH A;  4KKZ A;  5JPE A;  4XPN A;  3FLO A;  1FJM A;  3H63 A;  2O8G A;  1KBP A;  1T71 A;  5INB A;  3C5W C;  2WDE A;  5DNY A;  2IE3 C;  4FBW A;  1HP1 A;  1II7 A;  2HYP A;  4H2G A;  2BCD A;  2QFR A;  4O43 A;  2AHD A;  2Z06 A;  3H68 A;  2BQ8 X;  1OI8 A;  4O5G A;  3AV0 A;  2GJU A;  3E0J A;  3CK2 A;  1XZW A;  3N5U A;  3ZU0 A;  2JOG A;  3QFO A;  2ZOA A;  5C1V A;  2DXL A;  1MF8 A;  2Q8U A;  4LU9 A;  3ZTV A;  4UT3 B;  4I5L C;  3H62 B;  4HD0 A;  3AUZ A;  1OID A;  3H60 A;  3QFN A;  4KBP A;  1W24 A;  1V73 A;  4H2B A;  4JA9 A;  5B8I A;  3RL4 A;  3HVQ A;  3IB7 A;  3RQZ A;  4DSY A;  3EGG A;  4DHL A;  4MOY A;  3IB8 A;  3LL8 A;  3K7V C;  1UF3 A;  2ZBM A;  3H61 A;  1AUI A;  1XM7 A;  2WDF A;  4FCX A;  1IT6 A;  4ORC A;  4UT2 A;  2O8A A;  4FBK A;  4WWL A;  2NXF A;  2Z72 A;  3C9F A;  2BDX A;  3DSD A;  3RL3 A;  3E7A A;  4IL1 A;  4V0V A;  5F3W A;  3E7B A;  5GTU A;  3FGA C;  1HO5 A;  2WDD A;  4IYP C;  2R17 A;  2A22 A;  4ZVZ A;  4J6O A;  2CV9 A;  1UTE A;  3ICF A;  2HY1 A;  4H2I A;  2QFP A;  4NZV A;  5JPF A;  5J28 A;  3PSN A;  4LAC C;  4TUG A;  4V0W A;  2DFJ A;  1WAO 1;  4H1S A;  4UT3 A;  2QJC A;  1SU1 A;  2NYL C;  4O4K A;  3RL5 A;  3K7W C;  4B2O A;  1S70 A;  3DSC A;  2USH A;  4ORA A;  4G9J A;  3V4Y A;  3PSO A;  2YVT A;  3H69 A;  3QG5 C;  1TCO A;  2KKN A;  2NPP C;  1OIE A;  4F0Z A;  3EGH A;  3H66 A;  1G5B A;  4LTY A;  4ORB A;  3T1I A;  1S8E A;  3IVE A;  3P71 C;  4MOV A;  1S95 A;  2YEQ A;  2XMO A;  1QFC A;  3TGH A;  1U32 A;  1M63 A;  1QHW A;  5HPE A;  2NYM C;  3H67 A;  1HPU A;  2HYO A;  3KBP A;  3IVD A;  4M0V A;  1T70 A;  4TUI A;  1JK7 A;  2DXN A;  3GVE A;  3THO B;  4H1Y P; 
#chains in the Genus database with same CATH homology
 2ZO9 B;  2P6B A;  3DW8 C;  4I5N C;  4MP0 A;  4YKE A;  4ZX2 A;  2IE4 C;  5EQV A;  4OR9 A;  1USH A;  1S3M A;  3JYF A;  4JA7 A;  3D03 A;  3THN A;  1Z2X A;  1WAR A;  1S3N A;  4UWQ A;  3QFM A;  4FBQ A;  5JJT A;  2WDC A;  3H64 A;  2IAE C;  4H2F A;  4V0X A;  1S3L A;  2Z1A A;  3QFK A;  4O24 A;  1NNW A;  4DT2 A;  4Q7F A;  1Z2W A;  5IOH A;  4KKZ A;  5JPE A;  4XPN A;  3FLO A;  1FJM A;  3H63 A;  2O8G A;  1KBP A;  1T71 A;  5INB A;  3C5W C;  2WDE A;  5DNY A;  2IE3 C;  4FBW A;  1HP1 A;  1II7 A;  2HYP A;  4H2G A;  2BCD A;  2QFR A;  4O43 A;  2AHD A;  2Z06 A;  3H68 A;  2BQ8 X;  1OI8 A;  4O5G A;  3AV0 A;  2GJU A;  3E0J A;  3CK2 A;  1XZW A;  3N5U A;  3ZU0 A;  2JOG A;  3QFO A;  2ZOA A;  5C1V A;  2DXL A;  1MF8 A;  2Q8U A;  4LU9 A;  3ZTV A;  4UT3 B;  4I5L C;  3H62 B;  4HD0 A;  3AUZ A;  1OID A;  3H60 A;  3QFN A;  4KBP A;  1W24 A;  1V73 A;  4H2B A;  4JA9 A;  5B8I A;  3RL4 A;  3HVQ A;  3IB7 A;  3RQZ A;  4DSY A;  3EGG A;  4DHL A;  4MOY A;  3IB8 A;  3LL8 A;  3K7V C;  1UF3 A;  2ZBM A;  3H61 A;  1AUI A;  1XM7 A;  2WDF A;  4FCX A;  1IT6 A;  4ORC A;  4UT2 A;  2O8A A;  4FBK A;  4WWL A;  2NXF A;  2Z72 A;  3C9F A;  2BDX A;  3DSD A;  3RL3 A;  3E7A A;  4IL1 A;  4V0V A;  5F3W A;  3E7B A;  5GTU A;  3FGA C;  1HO5 A;  2WDD A;  4IYP C;  2R17 A;  2A22 A;  4ZVZ A;  4J6O A;  2CV9 A;  1UTE A;  3ICF A;  2HY1 A;  4H2I A;  2QFP A;  4NZV A;  5JPF A;  5J28 A;  3PSN A;  4LAC C;  4TUG A;  4V0W A;  2DFJ A;  1WAO 1;  4H1S A;  4UT3 A;  2QJC A;  1SU1 A;  2NYL C;  4O4K A;  3RL5 A;  3K7W C;  4B2O A;  1S70 A;  3DSC A;  2USH A;  4ORA A;  4G9J A;  3V4Y A;  3PSO A;  2YVT A;  3H69 A;  3QG5 C;  1TCO A;  2KKN A;  2NPP C;  1OIE A;  4F0Z A;  3EGH A;  3H66 A;  1G5B A;  4LTY A;  4ORB A;  3T1I A;  1S8E A;  3IVE A;  3P71 C;  4MOV A;  1S95 A;  2YEQ A;  2XMO A;  1QFC A;  3TGH A;  1U32 A;  1M63 A;  1QHW A;  5HPE A;  2NYM C;  3H67 A;  1HPU A;  2HYO A;  3KBP A;  3IVD A;  4M0V A;  1T70 A;  4TUI A;  1JK7 A;  2DXN A;  3GVE A;  3THO B;  4H1Y P; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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