1VBIA

Crystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus hb8
Total Genus 114
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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
114
sequence length
340
structure length
340
Chain Sequence
MRWRADFLSAWAEALLRKAGADEPSAKAVAWALVEADLRGVGSHGLLRLPVYVRRLEAGLVNPSPTLPLEERGPVALLDGEHGFGPRVALKAVEAAQSLARRHGLGAVGVRRSTHFGMAGLYAEKLAREGFVAWVTTNAEPDVVPFGGREKALGTNPLAFAAPAPQGILVADLATSESAMGKVFLAREKGERIPPSWGVDREGSPTDDPHRVYALRPLGGPKGYALALLVEVLSGVLTGAGVAHGIGRMYDEWDRPQDVGHFLLALDPGRFVGKEAFLERMGALWQALKATPPAPGHEEVFLPGELEARRRERALAEGMALPERVVAELKALGERYGVPW
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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 Type 2 malate/lactate dehydrogenase
publication title Crystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus HB8
rcsb
source organism Thermus thermophilus
total genus 114
structure length 340
sequence length 340
ec nomenclature ec 1.1.1.27: L-lactate dehydrogenase.
pdb deposition date 2004-02-27

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 1vbiA01
3.30.1370.60 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1 Hypothetical oxidoreductase yiak; domain 2 1vbiA02
1Z2IA 1X0AA 2CWFA 1WTJA 1NXUA 2CWHA 1VBIA 1V9NA 4FJSA 2X06A 2G8YA 4FJUA 3UOEA 1XRHA 3I0PA 1S20A 4H8AA
chains in the Genus database with same CATH superfamily
3V69A 3J81W 2PY9A 1V8CA 2LRRA 2M6QA 3JAMW 3KDGA 2UXDH 3J7AK 1J5EH 1S20A 2OPUA 1DTJA 2E5LH 1XMOH 4E9JA 1DT4A 1PQXA 1J5KA 1NXUA 2CWHA 4DV2H 4GKKH 1SEIA 2AXYA 2MJHA 2JE6I 2LTLA 2M8WA 3T1YH 4JVYA 1UG8A 1X4MA 4DUYH 5LMNH 4QMFB 4B3TH 2UXBH 1V9NA 2CPQA 2X06A 4DR7H 2PT7G 4BA2I 2OPVA 4YHHH 1HNZH 4LF8H 3U1KA 4X64H 1ZZJA 2F4VH 3QD7X 4AM3A 3KDKA 2CTKA 1HR0H 4NXNH 1EC6A 4NZRM 1N36H 4DUZH 2QNDA 4JV5H 4EC5A 1I94H 2HHHH 2ZQEA 2UUBH 3UOEA 4K0KH 5IT9W 2O4CA 4LF5H 4H8AA 4NXMH 2CTLA 1Z2IA 5JEAG 4DV6H 1WHRA 5LL6b 2FMRA 3T1HH 1FKAH 4B3SH 4LFCH 2CPMA 3GR5A 2P2RA 2CTEA 1N34H 1KHMA 2Z0SA 3OSSD 4JI0H 4NZTM 3EZJA 3GKUA 4AQYH 2UU9H 1VBIA 4DR2H 2BA0A 4FJUA 4GKJH 1XMQH 2E3UA 1TUAA 2FPHX 5DT9A 1K1GA 4DR6H 3VKEA 2JVZA 2CWFA 5BR8H 4DR4H 2LF0A 1XRHA 1HNWH 2FFMA 1XNQH 2UUAH 1ZZKA 4JI3H 1F0XA 4X62H 1ODHA 4B3RH 4LF9H 4WANA 3NCVA 4JI5H 4LF4H 2CTMA 1MSZA 5FLXW 4LFBH 4DV5H 1WTJA 3FAUA 2UXCH 2ZM6H 2ANRA 2PQUA 4DR1H 4NBQA 1N33H 2UUCH 4DV7H 1J4WA 4BA1I 4DV0H 4LFAH 1VIHA 5C0XG 2VQFH 4LF7H 3RF2A 2HH2A 1S03G 1IBLH 4X65H 2NN6G 4JVHA 4LIJA 4JI2H 1VIGA 3L7ZC 5A2QW 4WALA 2LTMA 2DGRA 1IBMH 1XNRH 1X4NA 1WVNA 4DV3H 2Y3MA 2CTJA 1IBKH 4LF6H 2BL5A 4JYAH 2JA9A 5IWAH 1X9ZA 3OTOH 4AIMA 2K1HA 4OX9H 1AN7A 4KHPH 4G08A 4JI1H 2VKCA 4YY3H 4OD6A 4DV1H 4FJSA 3SB1A 4B8TA 4JI6H 2HH3A 4X66H 1ZTGA 2YQRA 4PDBA 2JEAI 1X0AA 4B8CD 4DR3H 1I6UA 2CTFA 4IFDG 2JEBI 1FJGH 5K36G 4DV4H 3I0PA 2ANNA 4JI4H 2A1SA 4OCHA 3J80W 4B3MH 2D9IA 3GABA 4JI8H 1N32H 2VQEH 3AEVB 4DR5H 4JI7H 1WE8A 1ZZIA 2G8YA 2JZXA 4OO1G 1HNXH 5LMUH 3OETA
chains in the Genus database with same CATH topology
1Z2IA 1X0AA 2CWFA 1WTJA 1NXUA 2CWHA 1VBIA 1V9NA 4FJSA 2X06A 2G8YA 4FJUA 3UOEA 1XRHA 3I0PA 1S20A 4H8AA
chains in the Genus database with same CATH homology


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