2A2J | Genus

Total Genus 56

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	56
sequence length	203
structure length	202
Chain Sequence	PEKDGGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQPGS

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

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The Resolver thinks Pdb

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Time for openFile(/file/5cfc93a32987dda4bf0c2d98/pdb.gz): 1590 ms

reading 202 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

202 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:201});backbone only;select *;

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

Genus data interpretation

Chord Diagram

publication title	Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis. pubmed doi rcsb
molecule keywords	Pyridoxamine 5'-phosphate oxidase
molecule tags	Oxidoreductase
source organism	Mycobacterium tuberculosis
total genus	56
structure length	202
sequence length	203
chains with identical sequence	B
ec nomenclature	ec 1.4.3.5: Pyridoxal 5'-phosphate synthase.
pdb deposition date	2005-06-22

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01243	Putative_PNPOx	Pyridoxamine 5'-phosphate oxidase
A	PF10590	PNP_phzG_C	Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
2.30.110.10	Mainly Beta	Roll	Pnp Oxidase; Chain A	Electron Transport, Fmn-binding Protein; Chain A	2a2jA00

1W3RA 2HTDA 1YOAA 3U34A 3E4VA 3AWHA 3K87A 4F07A 3U0IA 1WLIA 2HHZA 3R5WA 1G77A 2FURA 1NRGA 4XHYA 3U35A 2Q9KA 4HMSA 3CP3A 2ASFA 4HMXA 1USCA 3DB0A 2RE7A 4IRAA 4R82A 5JABA 4Z85A 1USFA 1T9MA 1G78A 2ECRA 3EC6A 3HMZA 1FLMA 1RFEA 3K88A 3A6RA 2D5MA 2FHQA 3ZOCA 1YLNA 3ZOGA 3A20A 3CB0A 2I02A 2GJGA 3R5RA 4Y9IA 1W9AA 2X1KA 2HTIA 2RDEA 4ZKYA 1G79A 2ECUA 3GASA 2FG9A 2I51A 2R6VA 3BA3A 3FGEA 2HQ9A 2PTFA 2ED4A 1RZ1A 3F7EA 3VY2A 3VY5A 4XJ2A 1RZ0A 1W3PA 3AMFA 3ZODA 3R5YA 1WV4A 1XHNA 2E83A 5BNCA 1DNLA 1EJEA 3ZOHA 2QCKA 3U5WA 1AXJA 2QEAA 4QVBA 3H96A 3ZOEA 2VPAA 3IN6A 4HX6A 2X1JA 1W3QA 5CHOA 2A2JA 2R0XA 1Y30A 4L82A 3SWJA 2HQ7A 1VL7A 2D37A 2D38A 3DNHA 3KYFA 5ESCA 3NFWA 3FKHA 3HY8A 3BPKA 4HMUA 3R5ZA 3B5MA 2IABA 4HMWA 3BNKA 4HMVA 4HMTA 3ZOFA 1I0RA 1WLKA 1CI0A 5CHEC 3TGVA 3R5PA 3KYGA 2NR4A 3A6QA 4N7RC 2OL5A 1WGBA 3VYAA 3K86A 2ARZA 1XXOA 1TY9A 4YBNA 3R5LA 1W3OA 1JNWA 1I0SA 3DMBA 4YWNA 1G76A 2D36A 3PFTA 2IMLA 3RH7A 2AQ6A 2OU5A 2IG6A
chains in the Genus database with same CATH superfamily

3EAAA 1W3RA 2HTDA 1YOAA 3U34A 3E4VA 3AWHA 3K87A 4F07A 4MTKA 3U0IA 2GUJA 1WLIA 2HHZA 3R5WA 1G77A 2FURA 1NRGA 1Y12A 4XHYA 3U35A 2Q9KA 4HMSA 3CP3A 2ASFA 4HMXA 1USCA 2K4QA 3DB0A 2RE7A 4IRAA 4R82A 5JABA 4Z85A 1USFA 1T9MA 1G78A 2ECRA 3EC6A 3HMZA 4TV4A 1FLMA 1RFEA 3K88A 3A6RA 2D5MA 2FHQA 2L1TA 4UHVA 3ZOCA 1YLNA 3ZOGA 3A20A 3CB0A 2I02A 2GJGA 3R5RA 4Y9IA 1W9AA 3V4HA 2X1KA 2HTIA 2RDEA 4ZKYA 1G79A 2ECUA 3GASA 2FG9A 2I51A 2R6VA 3BA3A 3FGEA 2HQ9A 2PTFA 2ED4A 1RZ1A 3F7EA 3VY2A 3VY5A 4XJ2A 1RZ0A 1W3PA 3AMFA 3ZODA 3R5YA 1WV4A 1XHNA 2E83A 5BNCA 1DNLA 4W64A 1EJEA 3ZOHA 2QCKA 3U5WA 1AXJA 2QEAA 4QVBA 3H96A 3ZOEA 2VPAA 3IN6A 4HX6A 2X1JA 1W3QA 5CHOA 2A2JA 2R0XA 1Y30A 4L82A 3SWJA 2HQ7A 1VL7A 2D37A 2D38A 3DNHA 3KYFA 5ESCA 3NFWA 3FKHA 3HY8A 3BPKA 4HMUA 3R5ZA 3B5MA 2IABA 4HKHA 4HMWA 3BNKA 4HMVA 4HMTA 3ZOFA 1I0RA 2P5ZX 1WLKA 1CI0A 5CHEC 3TGVA 3R5PA 3KYGA 2NR4A 3A6QA 4N7RC 2OL5A 1WGBA 3VYAA 3K86A 2ARZA 1XXOA 1TY9A 4YBNA 3R5LA 1W3OA 3HE1A 1JNWA 1I0SA 3DMBA 4YWNA 1G76A 2D36A 3PFTA 2IMLA 3RH7A 2AQ6A 2OU5A 2IG6A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1W3R A;  2HTD A;  1YOA A;  3U34 A;  3E4V A;  3AWH A;  3K87 A;  4F07 A;  3U0I A;  1WLI A;  2HHZ A;  3R5W A;  1G77 A;  2FUR A;  1NRG A;  4XHY A;  3U35 A;  2Q9K A;  4HMS A;  3CP3 A;  2ASF A;  4HMX A;  1USC A;  3DB0 A;  2RE7 A;  4IRA A;  4R82 A;  5JAB A;  4Z85 A;  1USF A;  1T9M A;  1G78 A;  2ECR A;  3EC6 A;  3HMZ A;  1FLM A;  1RFE A;  3K88 A;  3A6R A;  2D5M A;  2FHQ A;  3ZOC A;  1YLN A;  3ZOG A;  3A20 A;  3CB0 A;  2I02 A;  2GJG A;  3R5R A;  4Y9I A;  1W9A A;  2X1K A;  2HTI A;  2RDE A;  4ZKY A;  1G79 A;  2ECU A;  3GAS A;  2FG9 A;  2I51 A;  2R6V A;  3BA3 A;  3FGE A;  2HQ9 A;  2PTF A;  2ED4 A;  1RZ1 A;  3F7E A;  3VY2 A;  3VY5 A;  4XJ2 A;  1RZ0 A;  1W3P A;  3AMF A;  3ZOD A;  3R5Y A;  1WV4 A;  1XHN A;  2E83 A;  5BNC A;  1DNL A;  1EJE A;  3ZOH A;  2QCK A;  3U5W A;  1AXJ A;  2QEA A;  4QVB A;  3H96 A;  3ZOE A;  2VPA A;  3IN6 A;  4HX6 A;  2X1J A;  1W3Q A;  5CHO A;  2A2J A;  2R0X A;  1Y30 A;  4L82 A;  3SWJ A;  2HQ7 A;  1VL7 A;  2D37 A;  2D38 A;  3DNH A;  3KYF A;  5ESC A;  3NFW A;  3FKH A;  3HY8 A;  3BPK A;  4HMU A;  3R5Z A;  3B5M A;  2IAB A;  4HMW A;  3BNK A;  4HMV A;  4HMT A;  3ZOF A;  1I0R A;  1WLK A;  1CI0 A;  5CHE C;  3TGV A;  3R5P A;  3KYG A;  2NR4 A;  3A6Q A;  4N7R C;  2OL5 A;  1WGB A;  3VYA A;  3K86 A;  2ARZ A;  1XXO A;  1TY9 A;  4YBN A;  3R5L A;  1W3O A;  1JNW A;  1I0S A;  3DMB A;  4YWN A;  1G76 A;  2D36 A;  3PFT A;  2IML A;  3RH7 A;  2AQ6 A;  2OU5 A;  2IG6 A; 
#chains in the Genus database with same CATH topology
 3EAA A;  1W3R A;  2HTD A;  1YOA A;  3U34 A;  3E4V A;  3AWH A;  3K87 A;  4F07 A;  4MTK A;  3U0I A;  2GUJ A;  1WLI A;  2HHZ A;  3R5W A;  1G77 A;  2FUR A;  1NRG A;  1Y12 A;  4XHY A;  3U35 A;  2Q9K A;  4HMS A;  3CP3 A;  2ASF A;  4HMX A;  1USC A;  2K4Q A;  3DB0 A;  2RE7 A;  4IRA A;  4R82 A;  5JAB A;  4Z85 A;  1USF A;  1T9M A;  1G78 A;  2ECR A;  3EC6 A;  3HMZ A;  4TV4 A;  1FLM A;  1RFE A;  3K88 A;  3A6R A;  2D5M A;  2FHQ A;  2L1T A;  4UHV A;  3ZOC A;  1YLN A;  3ZOG A;  3A20 A;  3CB0 A;  2I02 A;  2GJG A;  3R5R A;  4Y9I A;  1W9A A;  3V4H A;  2X1K A;  2HTI A;  2RDE A;  4ZKY A;  1G79 A;  2ECU A;  3GAS A;  2FG9 A;  2I51 A;  2R6V A;  3BA3 A;  3FGE A;  2HQ9 A;  2PTF A;  2ED4 A;  1RZ1 A;  3F7E A;  3VY2 A;  3VY5 A;  4XJ2 A;  1RZ0 A;  1W3P A;  3AMF A;  3ZOD A;  3R5Y A;  1WV4 A;  1XHN A;  2E83 A;  5BNC A;  1DNL A;  4W64 A;  1EJE A;  3ZOH A;  2QCK A;  3U5W A;  1AXJ A;  2QEA A;  4QVB A;  3H96 A;  3ZOE A;  2VPA A;  3IN6 A;  4HX6 A;  2X1J A;  1W3Q A;  5CHO A;  2A2J A;  2R0X A;  1Y30 A;  4L82 A;  3SWJ A;  2HQ7 A;  1VL7 A;  2D37 A;  2D38 A;  3DNH A;  3KYF A;  5ESC A;  3NFW A;  3FKH A;  3HY8 A;  3BPK A;  4HMU A;  3R5Z A;  3B5M A;  2IAB A;  4HKH A;  4HMW A;  3BNK A;  4HMV A;  4HMT A;  3ZOF A;  1I0R A;  2P5Z X;  1WLK A;  1CI0 A;  5CHE C;  3TGV A;  3R5P A;  3KYG A;  2NR4 A;  3A6Q A;  4N7R C;  2OL5 A;  1WGB A;  3VYA A;  3K86 A;  2ARZ A;  1XXO A;  1TY9 A;  4YBN A;  3R5L A;  1W3O A;  3HE1 A;  1JNW A;  1I0S A;  3DMB A;  4YWN A;  1G76 A;  2D36 A;  3PFT A;  2IML A;  3RH7 A;  2AQ6 A;  2OU5 A;  2IG6 A; 
#chains in the Genus database with same CATH homology
 1W3R A;  2HTD A;  1YOA A;  3U34 A;  3E4V A;  3AWH A;  3K87 A;  4F07 A;  3U0I A;  1WLI A;  2HHZ A;  3R5W A;  1G77 A;  2FUR A;  1NRG A;  4XHY A;  3U35 A;  2Q9K A;  4HMS A;  3CP3 A;  2ASF A;  4HMX A;  1USC A;  3DB0 A;  2RE7 A;  4IRA A;  4R82 A;  5JAB A;  4Z85 A;  1USF A;  1T9M A;  1G78 A;  2ECR A;  3EC6 A;  3HMZ A;  1FLM A;  1RFE A;  3K88 A;  3A6R A;  2D5M A;  2FHQ A;  3ZOC A;  1YLN A;  3ZOG A;  3A20 A;  3CB0 A;  2I02 A;  2GJG A;  3R5R A;  4Y9I A;  1W9A A;  2X1K A;  2HTI A;  2RDE A;  4ZKY A;  1G79 A;  2ECU A;  3GAS A;  2FG9 A;  2I51 A;  2R6V A;  3BA3 A;  3FGE A;  2HQ9 A;  2PTF A;  2ED4 A;  1RZ1 A;  3F7E A;  3VY2 A;  3VY5 A;  4XJ2 A;  1RZ0 A;  1W3P A;  3AMF A;  3ZOD A;  3R5Y A;  1WV4 A;  1XHN A;  2E83 A;  5BNC A;  1DNL A;  1EJE A;  3ZOH A;  2QCK A;  3U5W A;  1AXJ A;  2QEA A;  4QVB A;  3H96 A;  3ZOE A;  2VPA A;  3IN6 A;  4HX6 A;  2X1J A;  1W3Q A;  5CHO A;  2A2J A;  2R0X A;  1Y30 A;  4L82 A;  3SWJ A;  2HQ7 A;  1VL7 A;  2D37 A;  2D38 A;  3DNH A;  3KYF A;  5ESC A;  3NFW A;  3FKH A;  3HY8 A;  3BPK A;  4HMU A;  3R5Z A;  3B5M A;  2IAB A;  4HMW A;  3BNK A;  4HMV A;  4HMT A;  3ZOF A;  1I0R A;  1WLK A;  1CI0 A;  5CHE C;  3TGV A;  3R5P A;  3KYG A;  2NR4 A;  3A6Q A;  4N7R C;  2OL5 A;  1WGB A;  3VYA A;  3K86 A;  2ARZ A;  1XXO A;  1TY9 A;  4YBN A;  3R5L A;  1W3O A;  1JNW A;  1I0S A;  3DMB A;  4YWN A;  1G76 A;  2D36 A;  3PFT A;  2IML A;  3RH7 A;  2AQ6 A;  2OU5 A;  2IG6 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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2A2JA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations