1V9NA

Structure of malate dehydrogenase from pyrococcus horikoshii ot3
Total Genus 99
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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
99
sequence length
360
structure length
348
Chain Sequence
MFEKGYVDENYIRVPKDRLFSFIVRVLTKLGVPEEDAKIVADNLVMADLRGVESHGVQRLKRYVDGIISGGVNLHPKIRVIREGPSYALIDGDEGLGQVVGYRSMKLAIKKAKDTGIGIVIARNSNHYGIAGYYALMAAEEGMIGISMTNSRPLVAPTGGIERILGTNPIALAAPTKDKPFLLDMATSVVPIGKLEWAINREGNITTKVEEVFNGGALLPLGGFGELLGGHKGYGLSLMVDILSGILSGGTWSKYVKNTSEKGSNVCHFFMVIDIEHFIPLEEFKEKISQMIEEIKSSRKHPEFERIWIHGEKGFLTMETRLKLGIPIYRKVLEELNEIAKRVGVEGL
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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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molecule tags Oxidoreductase
molecule keywords Malate dehydrogenase
publication title Structure of Malate Dehydrogenase from Pyrococcus horikoshii OT3
rcsb
source organism Pyrococcus horikoshii
total genus 99
structure length 348
sequence length 360
ec nomenclature ec 1.1.1.37: Malate dehydrogenase.
pdb deposition date 2004-01-26

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02615 Ldh_2 Malate/L-lactate dehydrogenase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1530.10 Mainly Alpha Orthogonal Bundle Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 1v9nA01
3.30.1370.60 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1 Hypothetical oxidoreductase yiak; domain 2 1v9nA02
1X0AA 4FJUA 1V9NA 2X06A 4H8AA 2G8YA 3UOEA 1XRHA 1Z2IA 2CWHA 1S20A 3I0PA 4FJSA 1VBIA 1WTJA 1NXUA 2CWFA
chains in the Genus database with same CATH superfamily
1XNQH 4B3RH 4GKJH 4B3MH 4JYAH 1PQXA 1I94H 4LFCH 2JEAI 2JZXA 5A2QW 4FJSA 2PT7G 2F4VH 1XNRH 1AN7A 2UXCH 4WANA 4AQYH 3GKUA 2CTJA 3JAMW 2NN6G 1N33H 4DR3H 2ANRA 4NXMH 1IBLH 4EC5A 2LTLA 1X4MA 4OO1G 4JVHA 2UUBH 2DGRA 1Z2IA 1WE8A 2CWHA 2JVZA 3GR5A 3RF2A 4JI7H 4JI0H 2UUCH 2VQEH 4BA2I 3J7AK 1DTJA 2OPUA 3VKEA 1IBMH 4GKKH 2LRRA 5LMUH 1WTJA 4B3TH 2Y3MA 4X66H 2HH3A 1FKAH 3OSSD 3T1YH 1ODHA 4YHHH 2MJHA 4B3SH 1N32H 4IFDG 4LF8H 2A1SA 2CTKA 4X65H 3KDGA 4DV6H 4BA1I 4DR7H 2CPMA 4JI5H 1S03G 2ZQEA 2JE6I 2X06A 4DV5H 4DV3H 1HR0H 2BL5A 2FPHX 5IWAH 1FJGH 3QD7X 1WVNA 5C0XG 1K1GA 2HHHH 4QMFB 5LMNH 1ZZIA 1J5EH 2E5LH 4JI4H 4X62H 2FFMA 1X0AA 2CTEA 2YQRA 2VKCA 3EZJA 2CTMA 4X64H 3OTOH 1N36H 2OPVA 3GABA 1F0XA 4B8TA 1HNWH 2K1HA 1V8CA 2FMRA 1UG8A 4H8AA 4LFBH 1XRHA 4LIJA 3T1HH 1S20A 3I0PA 2AXYA 2P2RA 4OX9H 1J5KA 5FLXW 2HH2A 4E9JA 1V9NA 2G8YA 1VIHA 2JA9A 2ZM6H 2VQFH 4DUZH 5DT9A 1NXUA 4NBQA 4LF4H 3SB1A 1I6UA 2CPQA 5JEAG 4FJUA 1EC6A 2UU9H 2Z0SA 4DR2H 5BR8H 1ZZKA 4JI2H 4DR5H 4DV0H 4NXNH 2PY9A 1N34H 4AM3A 2M6QA 3NCVA 4DV7H 1IBKH 4DR4H 4OD6A 3AEVB 3J80W 1XMQH 4LF9H 3J81W 4LFAH 3OETA 4KHPH 1X4NA 1ZTGA 1KHMA 3UOEA 1VIGA 4DV1H 4DV4H 1VBIA 2CWFA 2D9IA 4OCHA 4JI8H 4PDBA 1MSZA 4DR6H 1X9ZA 4JI6H 1XMOH 4NZRM 4G08A 4DV2H 2BA0A 1ZZJA 2QNDA 4LF5H 1WHRA 2PQUA 4DR1H 4LF6H 2E3UA 3L7ZC 5LL6b 3FAUA 2CTFA 2M8WA 3V69A 2UUAH 2ANNA 3KDKA 1HNZH 4JI3H 4YY3H 2JEBI 4AIMA 2UXBH 5IT9W 4B8CD 3U1KA 4WALA 5K36G 4K0KH 1DT4A 1SEIA 4NZTM 4JVYA 1HNXH 1TUAA 1J4WA 2O4CA 4LF7H 2CTLA 2UXDH 4DUYH 2LTMA 4JI1H 2LF0A 4JV5H
chains in the Genus database with same CATH topology
1X0AA 4FJUA 1V9NA 2X06A 4H8AA 2G8YA 3UOEA 1XRHA 1Z2IA 2CWHA 1S20A 3I0PA 4FJSA 1VBIA 1WTJA 1NXUA 2CWFA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1X0A A;  4FJU A;  1V9N A;  2X06 A;  4H8A A;  2G8Y A;  3UOE A;  1XRH A;  1Z2I A;  2CWH A;  1S20 A;  3I0P A;  4FJS A;  1VBI A;  1WTJ A;  1NXU A;  2CWF A; 
#chains in the Genus database with same CATH topology
 1XNQ H;  4B3R H;  4GKJ H;  4B3M H;  4JYA H;  1PQX A;  1I94 H;  4LFC H;  2JEA I;  2JZX A;  5A2Q W;  4FJS A;  2PT7 G;  2F4V H;  1XNR H;  1AN7 A;  2UXC H;  4WAN A;  4AQY H;  3GKU A;  2CTJ A;  3JAM W;  2NN6 G;  1N33 H;  4DR3 H;  2ANR A;  4NXM H;  1IBL H;  4EC5 A;  2LTL A;  1X4M A;  4OO1 G;  4JVH A;  2UUB H;  2DGR A;  1Z2I A;  1WE8 A;  2CWH A;  2JVZ A;  3GR5 A;  3RF2 A;  4JI7 H;  4JI0 H;  2UUC H;  2VQE H;  4BA2 I;  3J7A K;  1DTJ A;  2OPU A;  3VKE A;  1IBM H;  4GKK H;  2LRR A;  5LMU H;  1WTJ A;  4B3T H;  2Y3M A;  4X66 H;  2HH3 A;  1FKA H;  3OSS D;  3T1Y H;  1ODH A;  4YHH H;  2MJH A;  4B3S H;  1N32 H;  4IFD G;  4LF8 H;  2A1S A;  2CTK A;  4X65 H;  3KDG A;  4DV6 H;  4BA1 I;  4DR7 H;  2CPM A;  4JI5 H;  1S03 G;  2ZQE A;  2JE6 I;  2X06 A;  4DV5 H;  4DV3 H;  1HR0 H;  2BL5 A;  2FPH X;  5IWA H;  1FJG H;  3QD7 X;  1WVN A;  5C0X G;  1K1G A;  2HHH H;  4QMF B;  5LMN H;  1ZZI A;  1J5E H;  2E5L H;  4JI4 H;  4X62 H;  2FFM A;  1X0A A;  2CTE A;  2YQR A;  2VKC A;  3EZJ A;  2CTM A;  4X64 H;  3OTO H;  1N36 H;  2OPV A;  3GAB A;  1F0X A;  4B8T A;  1HNW H;  2K1H A;  1V8C A;  2FMR A;  1UG8 A;  4H8A A;  4LFB H;  1XRH A;  4LIJ A;  3T1H H;  1S20 A;  3I0P A;  2AXY A;  2P2R A;  4OX9 H;  1J5K A;  5FLX W;  2HH2 A;  4E9J A;  1V9N A;  2G8Y A;  1VIH A;  2JA9 A;  2ZM6 H;  2VQF H;  4DUZ H;  5DT9 A;  1NXU A;  4NBQ A;  4LF4 H;  3SB1 A;  1I6U A;  2CPQ A;  5JEA G;  4FJU A;  1EC6 A;  2UU9 H;  2Z0S A;  4DR2 H;  5BR8 H;  1ZZK A;  4JI2 H;  4DR5 H;  4DV0 H;  4NXN H;  2PY9 A;  1N34 H;  4AM3 A;  2M6Q A;  3NCV A;  4DV7 H;  1IBK H;  4DR4 H;  4OD6 A;  3AEV B;  3J80 W;  1XMQ H;  4LF9 H;  3J81 W;  4LFA H;  3OET A;  4KHP H;  1X4N A;  1ZTG A;  1KHM A;  3UOE A;  1VIG A;  4DV1 H;  4DV4 H;  1VBI A;  2CWF A;  2D9I A;  4OCH A;  4JI8 H;  4PDB A;  1MSZ A;  4DR6 H;  1X9Z A;  4JI6 H;  1XMO H;  4NZR M;  4G08 A;  4DV2 H;  2BA0 A;  1ZZJ A;  2QND A;  4LF5 H;  1WHR A;  2PQU A;  4DR1 H;  4LF6 H;  2E3U A;  3L7Z C;  5LL6 b;  3FAU A;  2CTF A;  2M8W A;  3V69 A;  2UUA H;  2ANN A;  3KDK A;  1HNZ H;  4JI3 H;  4YY3 H;  2JEB I;  4AIM A;  2UXB H;  5IT9 W;  4B8C D;  3U1K A;  4WAL A;  5K36 G;  4K0K H;  1DT4 A;  1SEI A;  4NZT M;  4JVY A;  1HNX H;  1TUA A;  1J4W A;  2O4C A;  4LF7 H;  2CTL A;  2UXD H;  4DUY H;  2LTM A;  4JI1 H;  2LF0 A;  4JV5 H; 
#chains in the Genus database with same CATH homology
 1X0A A;  4FJU A;  1V9N A;  2X06 A;  4H8A A;  2G8Y A;  3UOE A;  1XRH A;  1Z2I A;  2CWH A;  1S20 A;  3I0P A;  4FJS A;  1VBI A;  1WTJ A;  1NXU A;  2CWF 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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