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


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