SMTL ID : 3vys.1

Crystal structure of the HypC-HypD-HypE complex (form I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain B: C.323, R.324, C.325, C.338, L.340, F.341, C.345, V.351, G.352, C.354, M.355, C.362 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.323, B:C.338, B:C.345, B:C.362 SF4.5: 12 residues within 4Å: Chain E: C.323, R.324, C.325, C.338, L.340, F.341, C.345, V.351, G.352, C.354, M.355, C.362 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.323, E:C.338, E:C.345, E:C.362

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain C: D.59, D.84, D.221 Ligands: MG.3 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.59, C:D.84, H2O.3 MG.3: 4 residues within 4Å: Chain C: D.43, D.84, D.221 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.43, C:D.84, C:D.221 MG.4: 6 residues within 4Å: Chain C: D.42, D.43, V.87, M.88, D.158, M.219 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.42, C:D.43, C:D.158, C:M.219 MG.6: 4 residues within 4Å: Chain F: D.59, D.84, D.221 Ligands: MG.7 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.59, F:D.84, H2O.7 MG.7: 4 residues within 4Å: Chain F: D.43, D.84, D.221 Ligands: MG.6 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.43, F:D.84, F:D.221 MG.8: 6 residues within 4Å: Chain F: D.42, D.43, V.87, M.88, D.158, M.219 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.42, F:D.43, F:D.158, F:M.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, S. et al., Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation. Structure (2012)

Release Date

2012-11-28

Peptides

Hydrogenase expression/formation protein HypC: AD
Hydrogenase expression/formation protein HypD: BE
Hydrogenase expression/formation protein HypE: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
C

F
C

Hydrogenase expression/formation protein HypC

Hydrogenase expression/formation protein HypD

Hydrogenase expression/formation protein HypE

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