SMTL ID : 5aup.1

Crystal structure of the HypAB complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.73, C.76, C.110, C.113 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.73, A:C.76, A:C.110, A:C.113 ZN.4: 4 residues within 4Å: Chain C: C.73, C.76, C.110, C.113 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.73, C:C.76, C:C.110, C:C.113

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 22 residues within 4Å: Chain B: G.29, G.30, V.31, G.32, K.33, S.34, L.35, D.57, P.135, N.187, M.188, I.216, P.217, Y.219, L.222, D.223, F.237 Chain D: K.28, G.29, S.160, L.162 Ligands: MG.3 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:G.30, B:V.31, B:G.32, B:K.33, B:K.33, B:S.34, B:S.34, B:L.35, B:N.187, B:P.217, B:Y.219, B:D.223, D:K.28, D:G.29, D:S.160, D:S.160 Water bridges: B:S.34, B:D.57, B:S.62, B:S.62, B:S.62 ACP.5: 23 residues within 4Å: Chain B: K.28, G.29, S.160, L.162 Chain D: G.29, G.30, V.31, G.32, K.33, S.34, L.35, D.57, P.135, N.187, M.188, I.216, P.217, F.218, Y.219, L.222, D.223, F.237 Ligands: MG.6 18 PLIP interactions: 3 interactions with chain B, 15 interactions with chain D Hydrogen bonds: B:G.29, B:S.160, B:S.160, D:G.30, D:V.31, D:G.32, D:K.33, D:K.33, D:K.33, D:S.34, D:L.35, D:D.57, D:N.187, D:P.217, D:Y.219, D:D.223 Water bridges: D:S.34, D:S.62

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: S.34, D.57 Ligands: ACP.2 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.34, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain D: S.34, D.57, D.132 Ligands: ACP.5 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.34, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, S. et al., Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-06-24

Peptides

Probable hydrogenase nickel incorporation protein HypA: AC
ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
H

B
B

D
I

Probable hydrogenase nickel incorporation protein HypA

ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog

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