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): 1413 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: 23 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

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

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

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