PDB entry 6kma

View 6kma on RCSB PDB site
Description: crystal structure of suca with glycolaldehyde-1-13c from vibrio vulnificus
Deposited on 2019-07-31, released 2020-08-05
The last revision was dated 2021-02-24, with a file datestamp of 2021-02-19.
Experiment type: XRAY
Resolution: 2.28 Å
R-factor: N/A
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
    Species: Vibrio vulnificus (strain CMCP6) [TaxId:216895]
    Gene: sucA, VV1_0157
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
    Species: Vibrio vulnificus (strain CMCP6) [TaxId:216895]
    Gene: sucA, VV1_0157
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
    Species: Vibrio vulnificus (strain CMCP6) [TaxId:216895]
    Gene: sucA, VV1_0157
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
    Species: Vibrio vulnificus (strain CMCP6) [TaxId:216895]
    Gene: sucA, VV1_0157
    Database cross-references and differences (RAF-indexed):
  • Heterogens: DW3, MG, TPP, P6G, CA, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6kmaA (A:)
mgsshhhhhhdydipttenlyfqggggggdvdakqvkvlqlinayrfrgheaaeldplgl
wqrptvaeldpafhnlteddfeetfnvgsfavgqetmplkdiytalkktycgsigaeymh
mtdteqkrwiqqrlesvvgqpsfdkdekrtflaeltaaeglerylgakfpgakrfslegg
damipmmkelirhagrsgmrevvigmahrgrlnmlvnvlgkkpqdlfdefagkhgeswgt
gdvkyhqgfsadfatpggdvhlalafnpshleivnpvvmgsvrarqdrlgdddgskvlpi
tihgdsaiagqgvvaetfnmsqargfcvggtvrvvvnnqvgfttsnprdtrstmyctdia
kmvqapifhvnaddpeavafvtrialdyrnefkrdvvidlvcyrrhghneadepnatqpl
myqkikkhptprklyadvlidrnecdietatqmvneyrdaldhgevvvkewrpmalhsvd
wspylghewdtpwsntydkqrlvelgkrlcqypeshtlhsrvsklyndrtamtngekeld
wgmaetlayatlvddgkririsgqdsgrgtffhrhavlhnqndastyvplanihdkqgpf
evfdsvlseeavlafeygyataepsgltlweaqfgdfangaqvvidqfissgeqkwarlc
gltmllphgyegqgpehssarlerylqlcaeqnmqvvvpstpaqvyhmirrqvvrpmrrp
livmspksllrhplctsslddlangtfmpaipeideldpakvkrvvfcsgkvyfdlleqr
rnneqddvaivrieqlypfpmddvkaaiapyvnvedfvwcqeepqnqgawycsqhnfraa
ipagtelkyagrpasaspavgymsvhlkqqkaliddalnvnektsd

    Sequence, based on observed residues (ATOM records):
    >6kmaA (A:)
vdakqvkvlqlinayrfrgheaaeldplglwqrptvaeldpafhnlteddfeetfnvgsf
avgqetmplkdiytalkktycgsigaeymhmtdteqkrwiqqrlesvvgqpsfdkdekrt
flaeltaaeglerylgakfpgakrfsleggdamipmmkelirhagrsgmrevvigmahrg
rlnmlvnvlgkkpqdlfdefagkhwgtgdvkyhqgfsadfatpggdvhlalafnpshlei
vnpvvmgsvrarqdrlgdddgskvlpitihgdsaiagqgvvaetfnmsqargfcvggtvr
vvvnnqvgfttsnprdtrstmyctdiakmvqapifhvnaddpeavafvtrialdyrnefk
rdvvidlvcyrrhghneadepnatqplmyqkikkhptprklyadvlidrnecdietatqm
vneyrdaldhgevvvkewrpmaylghewdtpwsntydkqrlvelgkrlcqypeshtlhsr
vsklyndrtamtngekeldwgmaetlayatlvddgkririsgqdsgrgtffhrhavlhnq
ndastyvplanihdkqgpfevfdsvlseeavlafeygyataepsgltlweaqfgdfanga
qvvidqfissgeqkwarlcgltmllphgyegqgpehssarlerylqlcaeqnmqvvvpst
paqvyhmirrqvvrpmrrplivmspksllrhplctsslddlangtfmpaipeideldpak
vkrvvfcsgkvyfdlleqrrnneqddvaivrieqlypfpmddvkaaiapyvnvedfvwcq
eepqnqgawycsqhnfraaipagtelkyagrpasaspavgymsvhlkqqkaliddalnv

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6kmaB (B:)
mgsshhhhhhdydipttenlyfqggggggdvdakqvkvlqlinayrfrgheaaeldplgl
wqrptvaeldpafhnlteddfeetfnvgsfavgqetmplkdiytalkktycgsigaeymh
mtdteqkrwiqqrlesvvgqpsfdkdekrtflaeltaaeglerylgakfpgakrfslegg
damipmmkelirhagrsgmrevvigmahrgrlnmlvnvlgkkpqdlfdefagkhgeswgt
gdvkyhqgfsadfatpggdvhlalafnpshleivnpvvmgsvrarqdrlgdddgskvlpi
tihgdsaiagqgvvaetfnmsqargfcvggtvrvvvnnqvgfttsnprdtrstmyctdia
kmvqapifhvnaddpeavafvtrialdyrnefkrdvvidlvcyrrhghneadepnatqpl
myqkikkhptprklyadvlidrnecdietatqmvneyrdaldhgevvvkewrpmalhsvd
wspylghewdtpwsntydkqrlvelgkrlcqypeshtlhsrvsklyndrtamtngekeld
wgmaetlayatlvddgkririsgqdsgrgtffhrhavlhnqndastyvplanihdkqgpf
evfdsvlseeavlafeygyataepsgltlweaqfgdfangaqvvidqfissgeqkwarlc
gltmllphgyegqgpehssarlerylqlcaeqnmqvvvpstpaqvyhmirrqvvrpmrrp
livmspksllrhplctsslddlangtfmpaipeideldpakvkrvvfcsgkvyfdlleqr
rnneqddvaivrieqlypfpmddvkaaiapyvnvedfvwcqeepqnqgawycsqhnfraa
ipagtelkyagrpasaspavgymsvhlkqqkaliddalnvnektsd

    Sequence, based on observed residues (ATOM records):
    >6kmaB (B:)
dakqvkvlqlinayrfrgheaaeldplglwqrptvaeldpafhnlteddfeetfnvgsfa
vgqetmplkdiytalkktycgsigaeymhmtdteqkrwiqqrlesvvgqpsfdkdekrtf
laeltaaeglerylgakfpgakrfsleggdamipmmkelirhagrsgmrevvigmahrgr
lnmlvnvlgkkpqdlfdefagkwgtgdvkyhqgfsadfatpggdvhlalafnpshleivn
pvvmgsvrarqdrlgdddgskvlpitihgdsaiagqgvvaetfnmsqargfcvggtvrvv
vnnqvgfttsnprdtrstmyctdiakmvqapifhvnaddpeavafvtrialdyrnefkrd
vvidlvcyrrhghneadepnatqplmyqkikkhptprklyadvlidrnecdietatqmvn
eyrdaldhgevvvkewrpmaylghewdtpwsntydkqrlvelgkrlcqypeshtlhsrvs
klyndrtamtngekeldwgmaetlayatlvddgkririsgqdsgrgtffhrhavlhnqnd
astyvplanihdkqgpfevfdsvlseeavlafeygyataepsgltlweaqfgdfangaqv
vidqfissgeqkwarlcgltmllphgyegqgpehssarlerylqlcaeqnmqvvvpstpa
qvyhmirrqvvrpmrrplivmspksllrhplctsslddlangtfmpaipeideldpakvk
rvvfcsgkvyfdlleqrrnneqddvaivrieqlypfpmddvkaaiapyvnvedfvwcqee
pqnqgawycsqhnfraaipagtelkyagrpasaspavgymsvhlkqqkaliddalnv

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6kmaC (C:)
mgsshhhhhhdydipttenlyfqggggggdvdakqvkvlqlinayrfrgheaaeldplgl
wqrptvaeldpafhnlteddfeetfnvgsfavgqetmplkdiytalkktycgsigaeymh
mtdteqkrwiqqrlesvvgqpsfdkdekrtflaeltaaeglerylgakfpgakrfslegg
damipmmkelirhagrsgmrevvigmahrgrlnmlvnvlgkkpqdlfdefagkhgeswgt
gdvkyhqgfsadfatpggdvhlalafnpshleivnpvvmgsvrarqdrlgdddgskvlpi
tihgdsaiagqgvvaetfnmsqargfcvggtvrvvvnnqvgfttsnprdtrstmyctdia
kmvqapifhvnaddpeavafvtrialdyrnefkrdvvidlvcyrrhghneadepnatqpl
myqkikkhptprklyadvlidrnecdietatqmvneyrdaldhgevvvkewrpmalhsvd
wspylghewdtpwsntydkqrlvelgkrlcqypeshtlhsrvsklyndrtamtngekeld
wgmaetlayatlvddgkririsgqdsgrgtffhrhavlhnqndastyvplanihdkqgpf
evfdsvlseeavlafeygyataepsgltlweaqfgdfangaqvvidqfissgeqkwarlc
gltmllphgyegqgpehssarlerylqlcaeqnmqvvvpstpaqvyhmirrqvvrpmrrp
livmspksllrhplctsslddlangtfmpaipeideldpakvkrvvfcsgkvyfdlleqr
rnneqddvaivrieqlypfpmddvkaaiapyvnvedfvwcqeepqnqgawycsqhnfraa
ipagtelkyagrpasaspavgymsvhlkqqkaliddalnvnektsd

    Sequence, based on observed residues (ATOM records):
    >6kmaC (C:)
vdakqvkvlqlinayrfrgheaaeldplglwqrptvaeldpafhnlteddfeetfnvgsf
avgqetmplkdiytalkktycgsigaeymhmtdteqkrwiqqrlesvvgqpsfdkdekrt
flaeltaaeglerylgakfpgakrfsleggdamipmmkelirhagrsgmrevvigmahrg
rlnmlvnvlgkkpqdlfdefagkswgtgdvkyhqgfsadfatpggdvhlalafnpshlei
vnpvvmgsvrarqdrlgdddgskvlpitihgdsaiagqgvvaetfnmsqargfcvggtvr
vvvnnqvgfttsnprdtrstmyctdiakmvqapifhvnaddpeavafvtrialdyrnefk
rdvvidlvcyrrhghneadepnatqplmyqkikkhptprklyadvlidrnecdietatqm
vneyrdaldhgevvvkewrpmaylghewdtpwsntydkqrlvelgkrlcqypeshtlhsr
vsklyndrtamtngekeldwgmaetlayatlvddgkririsgqdsgrgtffhrhavlhnq
ndastyvplanihdkqgpfevfdsvlseeavlafeygyataepsgltlweaqfgdfanga
qvvidqfissgeqkwarlcgltmllphgyegqgpehssarlerylqlcaeqnmqvvvpst
paqvyhmirrqvvrpmrrplivmspksllrhplctsslddlangtfmpaipeideldpak
vkrvvfcsgkvyfdlleqrrnneqddvaivrieqlypfpmddvkaaiapyvnvedfvwcq
eepqnqgawycsqhnfraaipagtelkyagrpasaspavgymsvhlkqqkaliddalnv

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6kmaD (D:)
mgsshhhhhhdydipttenlyfqggggggdvdakqvkvlqlinayrfrgheaaeldplgl
wqrptvaeldpafhnlteddfeetfnvgsfavgqetmplkdiytalkktycgsigaeymh
mtdteqkrwiqqrlesvvgqpsfdkdekrtflaeltaaeglerylgakfpgakrfslegg
damipmmkelirhagrsgmrevvigmahrgrlnmlvnvlgkkpqdlfdefagkhgeswgt
gdvkyhqgfsadfatpggdvhlalafnpshleivnpvvmgsvrarqdrlgdddgskvlpi
tihgdsaiagqgvvaetfnmsqargfcvggtvrvvvnnqvgfttsnprdtrstmyctdia
kmvqapifhvnaddpeavafvtrialdyrnefkrdvvidlvcyrrhghneadepnatqpl
myqkikkhptprklyadvlidrnecdietatqmvneyrdaldhgevvvkewrpmalhsvd
wspylghewdtpwsntydkqrlvelgkrlcqypeshtlhsrvsklyndrtamtngekeld
wgmaetlayatlvddgkririsgqdsgrgtffhrhavlhnqndastyvplanihdkqgpf
evfdsvlseeavlafeygyataepsgltlweaqfgdfangaqvvidqfissgeqkwarlc
gltmllphgyegqgpehssarlerylqlcaeqnmqvvvpstpaqvyhmirrqvvrpmrrp
livmspksllrhplctsslddlangtfmpaipeideldpakvkrvvfcsgkvyfdlleqr
rnneqddvaivrieqlypfpmddvkaaiapyvnvedfvwcqeepqnqgawycsqhnfraa
ipagtelkyagrpasaspavgymsvhlkqqkaliddalnvnektsd

    Sequence, based on observed residues (ATOM records):
    >6kmaD (D:)
dakqvkvlqlinayrfrgheaaeldplglwqrptvaeldpafhnlteddfeetfnvgsfa
vgqetmplkdiytalkktycgsigaeymhmtdteqkrwiqqrlesvvgqpsfdkdekrtf
laeltaaeglerylgakfpgakrfsleggdamipmmkelirhagrsgmrevvigmahrgr
lnmlvnvlgkkpqdlfdefagkgtgdvkyhqgfsadfatpggdvhlalafnpshleivnp
vvmgsvrarqdrlgdddgskvlpitihgdsaiagqgvvaetfnmsqargfcvggtvrvvv
nnqvgfttsnprdtrstmyctdiakmvqapifhvnaddpeavafvtrialdyrnefkrdv
vidlvcyrrhghneadepnatqplmyqkikkhptprklyadvlidrnecdietatqmvne
yrdaldhgevvvkewrpmaylghewdtpwsntydkqrlvelgkrlcqypeshtlhsrvsk
lyndrtamtngekeldwgmaetlayatlvddgkririsgqdsgrgtffhrhavlhnqnda
styvplanihdkqgpfevfdsvlseeavlafeygyataepsgltlweaqfgdfangaqvv
idqfissgeqkwarlcgltmllphgyegqgpehssarlerylqlcaeqnmqvvvpstpaq
vyhmirrqvvrpmrrplivmspksllrhplctsslddlangtfmpaipeideldpakvkr
vvfcsgkvyfdlleqrrnneqddvaivrieqlypfpmddvkaaiapyvnvedfvwcqeep
qnqgawycsqhnfraaipagtelkyagrpasaspavgymsvhlkqqkaliddalnv