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The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)

X-ray diffraction
1.75Å resolution
PDB entry 2b0j coloured by chain, front view.
PDB entry 2b0j coloured by chain, side view.
PDB entry 2b0j coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Assembly composition:
homo dimer (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: 5,10-methenyltetrahydromethanopterin hydrogenase
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Multimeric state: homo dimer
Accessible surface area: 25913.68 Å2
Buried surface area: 8132.96 Å2
Dissociation area: 4,066.48 Å2
Dissociation energy (ΔGdiss): 75.93 kcal/mol
Dissociation entropy (TΔSdiss): 14.65 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-176577
Homo dimeric assembly 1 of PDB entry 2b0j coloured by chemically distinct molecules, front view.
Homo dimeric assembly 1 of PDB entry 2b0j coloured by chemically distinct molecules, side view.
Homo dimeric assembly 1 of PDB entry 2b0j coloured by chemically distinct molecules, top view.
    Assembly 1
Confidence : 9%
No. subunits : 2
Symmetry : C2
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3DComplex & QSbio predictionx
No. subunits : 2
Symmetry : C2
Evidence : Sequence is/are identical to 3f47_1 (which is supposedly correct) but the structure appears to be different (TM-score=NA). This might reflect that a wrong interface was inferred in its reconstruction, but might also be caused by a large conformational change

Macromolecules

5,10-methenyltetrahydromethanopterin hydrogenase
Chain: A
Length: 358 amino acids
Theoretical weight: 38.74 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58194 (Residues: 1-358; Coverage: 100%)
Gene names: MJ0784, hmd
Pfam:
InterPro:
CATH:
SCOP:
5,10-methenyltetrahydromethanopterin hydrogenase in PDB entry 2b0j, assembly 1, front view.
5,10-methenyltetrahydromethanopterin hydrogenase in PDB entry 2b0j, assembly 1, side view.
5,10-methenyltetrahydromethanopterin hydrogenase in PDB entry 2b0j, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q58194  
135850100150200250300350
 
100200300MKIAILGAGCYRTHAAAGITNFMRACEVAKEVGKPEIALTHSSITYGAELLHLVPDVKEVIVSDPCFAEEPGLVVIDEFDPKEVMEAHLSGNPESIMPKIREVVKAKAKELPKPPKACIHLVHPEDVGLKVTSDDREAVEGADIVITWLPKGNKQPDIIKKFADAIPEGAIVTHACTIPTTKFAKIFKDLGREDLNITSYHPGCVPEMKGQVYIAEGYASEEAVNKLYEIGKIARGKAFKMPANLIGPVCDMCSAVTATVYAGLLAYRDAVTKILGAPADFAQMMADEALTQIHNLMKEKGIANMEEALDPAALLGTADSMCFGPLAEILPTALKVLEKHKVVEEEGKTKCEIMSQKE
UniProt
Q58194
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Interaction interfaces
Sequence conservation
Molecule details ›

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