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


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