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5d06 › Structure analysis

Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme

X-ray diffraction

3.1Å resolution

PDB entry 5d06 coloured by chain, front view.

PDB entry 5d06 coloured by chain, side view.

PDB entry 5d06 coloured by chain, top view.

Source organism: [Candida] glabrata CBS 138

Assembly composition:

monomeric (preferred)

Entry contents: 1 distinct polypeptide molecule

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5d06 overview
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Assembly composition XML
Assembly 1 (mmCIF; gz)
Assembly 2 (mmCIF; gz)
Assembly 1 (atom only; mmCIF)
Assembly 2 (atom only; mmCIF)
Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
PDB file (gz)
PDBML
PDBML (ATOM lines)
PDBML (no atoms)
Structure Factors
EDS map
EDS difference map
FASTA (Entry)

Assemblies

Assembly 1 (preferred)

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Assembly Name: Glycogen debranching enzyme
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Multimeric state: monomeric

Accessible surface area: 60015.38 Å²

Buried surface area: 0.0 Å²

Dissociation area: 0 Å²

Dissociation energy (ΔG^diss): 0 kcal/mol

Dissociation entropy (TΔS^diss): 0 kcal/mol

Symmetry number: 1

PDBe Complex ID: PDB-CPX-179626

Monomeric assembly 1 of PDB entry 5d06 coloured by chemically distinct molecules, front view.

Monomeric assembly 1 of PDB entry 5d06 coloured by chemically distinct molecules, side view.

Monomeric assembly 1 of PDB entry 5d06 coloured by chemically distinct molecules, top view.

Monomeric assembly 1 of PDB entry 5d06 coloured by chemically distinct molecules, front view.

Monomeric assembly 1 of PDB entry 5d06 coloured by chemically distinct molecules, side view.

Monomeric assembly 1 of PDB entry 5d06 coloured by chemically distinct molecules, top view.

Error: API request failed!

Assembly 2

Download 3D Visualisation

Assembly Name: Glycogen debranching enzyme
hide full assembly name

Multimeric state: monomeric

Accessible surface area: 61419.71 Å²

Buried surface area: 0.0 Å²

Dissociation area: 0 Å²

Dissociation energy (ΔG^diss): 0 kcal/mol

Dissociation entropy (TΔS^diss): 0 kcal/mol

Symmetry number: 1

PDBe Complex ID: PDB-CPX-179626

Monomeric assembly 2 of PDB entry 5d06 coloured by chemically distinct molecules, front view.

Monomeric assembly 2 of PDB entry 5d06 coloured by chemically distinct molecules, side view.

Monomeric assembly 2 of PDB entry 5d06 coloured by chemically distinct molecules, top view.

Monomeric assembly 2 of PDB entry 5d06 coloured by chemically distinct molecules, front view.

Monomeric assembly 2 of PDB entry 5d06 coloured by chemically distinct molecules, side view.

Monomeric assembly 2 of PDB entry 5d06 coloured by chemically distinct molecules, top view.

Error: API request failed!

Macromolecules

Glycogen debranching enzyme

Chains: A, B
Length: 1528 amino acids
Theoretical weight: 174.47 KDa
Source organism: [Candida] glabrata CBS 138
Expression system: Escherichia coli
UniProt:

Canonical: Q6FSK0 (Residues: 1-1528; Coverage: 100%)

Gene names: CAGL0G09977g, GDB1
Pfam:

N-terminal domain from the human glycogen debranching enzyme
Glycogen debranching enzyme, glucanotransferase domain
Central domain of human glycogen debranching enzyme
Amylo-alpha-1,6-glucosidase

InterPro:

Glycogen debranching enzyme
Glycogen debranching enzyme, metazoa
Eukaryotic glycogen debranching enzyme, N-terminal domain
Glycogen debranching enzyme, glucanotransferase domain
Glycoside hydrolase superfamily
Glycogen debranching enzyme, central domain
Glycogen debranching enzyme, C-terminal
Six-hairpin glycosidase superfamily
Six-hairpin glycosidase-like superfamily

Glycogen debranching enzyme in PDB entry 5d06, assembly 1, front view.

Glycogen debranching enzyme in PDB entry 5d06, assembly 1, side view.

Glycogen debranching enzyme in PDB entry 5d06, assembly 1, top view.

FASTA Sequence


    >pdb|5d06|A B

MSAHRTLLLRLSDSGEPVTSCSYGQGVLTLPSLPLPQGKKLGDMPVYTVKLAIPAGSPVTRDGLIWTNCPPDFSTQFDREKFYKKIIKTSFHEDDHIDLDIYVPGTYCFYLSFKNDKDELETTRKFYFVVLPILSVNDKFIPLNSIAMQSVVSKWMGPTIKDWEKVFARVASKKYNMIHFTPLQHRGESNSPYSIYDQLEFDPTVFKSEKEVADMVERLRTEHNILSLTDIVFNHTANNSQWLLDHPEAGYNHKTSPHLISAIELDKKLLDFSEQMEALGYPVDLKTVDDLIKVMDGIKEHVIGELKLWEFYVVDVKQTVSELREKWGNSKSWSDDNIPSKDDSTNLAQFVRDNATEPGFGSLGERGSNKINIDKFAAILKKLHSEDYNNGIEELATKILNDINLPFYKEYDDDINEVLEQLFNRIKYLRIDDHGPKQGPITKKLPLSEPYFTRFKAKDGEEYALANNGWIWDGNPLVDFASSQSKAYLRREVIVWGDCVKLRYGKGPSDSPYLWERMSKYVEMNARIFNGFRIDNCHSTPLHVGQYFLDVARRVNPNLYVVAELFSGSEAMDCLFVERLGISSLIREAMQAWSEEELSRLVHRHGGRPIGSYKFVPLDDFPYPADVKIDEEYCAYNPDDHSVKCVSEIMIPKTLTATPPHALFMDCTHDNETPNQKRTVEDTLPNAALVAFCSSAIGSVYGYDEVFPQLLDLVQEKRTYSCAENTGISKVKTLLNNMREEIASEAVDIEDSEMHVHHDGQYITFHRTNAKNGKGWYLVARTKFHSSGDQMLPRIKLSQTKATFKAAFSLERTGDAPISDEIIEGIPTKLRELTGFDIGFDENTKETSILLPQDFPQGSIVIFETQQLGIDDSLDHFIRSGAIKATEKLSLESINYVLYRAEQEEYDYSEGRSGAYDIPDYGKPVYCGLQGWVSILRKIIFYNDLAHPLSNNLRNGHWAVDYVVNRLDLYKDKEGVAEVQEWLRSRMERIKQLPSYLVPSFFALVVGIMYGCCRLRAMQLMSDNVGKSTVFVQSLAMTSIQMVSAMKSTSILPDQNIAAMAAGLPHFSTNYMRCWGRDVFISLRGLLLTTGRYEEAKEHILAFAKTLKHGLIPNLLDAGRNPRYNARDAAWFFVQAIQDYVTIVPGGVSLLQEKVTRRFPLDDEYIPYDDPKAFSYSSTIEEIIYEILNRHAGGIKYREANAGPNLDRVMKDEGFNVEVNVDWETGLIHGGSQFNCGTWMDKMGESEKANSVGVPGTPRDGAAVEINGLLKSCLRFVLQLSKDGKFKYTEVTKPDGSKISLSSWNDLLQENFERCFYVPKNKEDDNKFEIDATIINRRGIYKDLYRSGKPYEDYQFRPNFTIAMVVAPELFTPDYAAGAIELADQVLRGPVGMRTLDPSDYNYRPYYNNGEDSDDFATSKGRNYHQGPEWVWCYGYFIRAYHYFNFLTNPKCQVEGSAKKLKPSSYLYRKLYSRLLKHREWIENSPWAGLAELTNKDGEVCNDSSPTQAWSTGCLLDLFYDLWISYEE

PDBe-KB: UniProt Coverage View: Q6FSK0

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UniProt

Q6FSK0

Mapping to UniProt Q6FSK0_CANGA

Chains

RSRZ Outlier Chain A

Chain A

RSRZ Outlier Chain B

Chain B

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Amino acid probabilities The amino acid probabilities are calculated using HMM profiles based on multiple sequence alignments. Click to see more details...

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Molecule details ›

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FASTA (Protein chains A, B)
Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
PDB file (gz)
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PDBML (ATOM lines)
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Structure Factors
SIFTS XML file with residue-level mappings

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BLAST Q6FSK0 (UniProt)

Quick links

5d06 overview
- Citations
Structure analysis
Function and Biology
Ligands and Environments
Experiments and Validation

Downloads

Close

Assembly composition XML
Assembly 1 (mmCIF; gz)
Assembly 2 (mmCIF; gz)
Assembly 1 (atom only; mmCIF)
Assembly 2 (atom only; mmCIF)
Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
PDB file (gz)
PDBML
PDBML (ATOM lines)
PDBML (no atoms)
Structure Factors
EDS map
EDS difference map
FASTA (Entry)

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