SMTL ID : 3vyt.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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 SF4.8: 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

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain C: D.59, D.84 Ligands: MG.3, CL.5, MG.6, MG.7 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.59, C:D.84, H2O.3, H2O.6 MG.3: 5 residues within 4Å: Chain C: D.43, D.84, D.221 Ligands: MG.2, MG.6 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.43, C:D.84, C:D.221, H2O.3, H2O.4 MG.4: 6 residues within 4Å: Chain C: D.42, D.43, V.87, M.88, D.158, M.219 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.42, C:D.43, C:D.158, C:M.219, H2O.4 MG.6: 6 residues within 4Å: Chain C: D.43, D.59, D.84 Ligands: MG.2, MG.3, MG.7 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain C: D.59, R.224 Chain F: D.132 Ligands: MG.2, CL.5, MG.6 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: F:D.132, C:D.59, H2O.3 MG.9: 6 residues within 4Å: Chain F: D.59, D.84 Ligands: MG.10, CL.12, MG.13, MG.14 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.59, F:D.84, H2O.9, H2O.12 MG.10: 5 residues within 4Å: Chain F: D.43, D.84, D.221 Ligands: MG.9, MG.13 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.43, F:D.84, F:D.221, H2O.9, H2O.10 MG.11: 6 residues within 4Å: Chain F: D.42, D.43, V.87, M.88, D.158, M.219 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.42, F:D.43, F:D.158, F:M.219, H2O.10 MG.13: 6 residues within 4Å: Chain F: D.43, D.59, D.84 Ligands: MG.9, MG.10, MG.14 No protein-ligand interaction detected (PLIP) MG.14: 6 residues within 4Å: Chain C: D.132 Chain F: D.59, R.224 Ligands: MG.9, CL.12, MG.13 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: C:D.132, F:D.59, H2O.9

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain C: D.59, T.223, R.224 Ligands: MG.2, MG.7 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain F: D.59, T.223, R.224 Ligands: MG.9, MG.14 Ligand excluded by PLIP

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

Related Entries With Identical Sequence