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


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