SMTL ID : 5aun.1

Crystal structure of the HypAB-Ni complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 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.12: 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 NI: NICKEL (II) ION(Non-covalent)

NI.2: 4 residues within 4Å: Chain A: M.1, H.2, E.3, H.98 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.2, A:H.98 NI.13: 4 residues within 4Å: Chain C: M.1, H.2, E.3, H.98 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.2, C:H.98

6 x URE: UREA(Non-functional Binders)

URE.3: 7 residues within 4Å: Chain A: E.35, L.36, D.38, L.82, K.94, I.97, H.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.38, A:K.94 URE.4: 2 residues within 4Å: Chain A: E.41, F.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.41 Water bridges: A:F.64 URE.5: 4 residues within 4Å: Chain A: R.30, G.130, I.131, K.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.30 Water bridges: A:G.130, A:I.131, A:I.131, A:K.132 URE.14: 7 residues within 4Å: Chain C: E.35, L.36, D.38, L.82, K.94, I.97, H.98 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.38, C:K.94 URE.15: 2 residues within 4Å: Chain C: E.41, F.64 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.41 Water bridges: C:F.64 URE.16: 4 residues within 4Å: Chain C: R.30, G.130, I.131, K.132 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.30 Water bridges: C:G.130, C:I.131, C:I.131, C:K.132

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

CL.6: 3 residues within 4Å: Chain A: Q.19, T.55, I.56 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain C: Q.19, T.55, I.56 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: Y.127 Chain D: A.3, D.5 No protein-ligand interaction detected (PLIP) GOL.11: 2 residues within 4Å: Chain B: R.79 Chain C: W.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.79 Water bridges: B:R.79 GOL.18: 3 residues within 4Å: Chain B: A.3, D.5 Chain C: Y.127 No protein-ligand interaction detected (PLIP) GOL.22: 2 residues within 4Å: Chain A: W.4 Chain D: R.79 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.79 Water bridges: D:R.79

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.8: 19 residues within 4Å: Chain B: G.30, V.31, G.32, K.33, S.34, L.35, N.187, M.188, I.216, P.217, F.218, Y.219, L.222, V.226, F.237 Chain D: K.28, S.160, L.162 Ligands: MG.9 23 PLIP interactions: 9 interactions with chain D, 14 interactions with chain B Hydrogen bonds: D:S.160, D:S.160, B:G.30, B:V.31, B:G.32, B:K.33, B:S.34, B:L.35, B:N.187, B:P.217, B:Y.219 Water bridges: D:K.28, D:K.28, D:K.28, D:K.28, D:L.162, B:K.33, B:K.33, B:K.33, B:K.33 Salt bridges: D:K.28, D:K.28, B:K.33 ADP.19: 19 residues within 4Å: Chain B: K.28, S.160, L.162 Chain D: G.30, V.31, G.32, K.33, S.34, L.35, N.187, M.188, I.216, P.217, F.218, Y.219, L.222, V.226, F.237 Ligands: MG.20 23 PLIP interactions: 14 interactions with chain D, 9 interactions with chain B Hydrogen bonds: D:G.30, D:V.31, D:G.32, D:K.33, D:S.34, D:L.35, D:N.187, D:P.217, D:Y.219, B:S.160, B:S.160 Water bridges: D:K.33, D:K.33, D:K.33, D:K.33, B:K.28, B:K.28, B:K.28, B:K.28, B:L.162 Salt bridges: D:K.33, B:K.28, B:K.28

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain B: S.34, D.57 Ligands: ADP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.34, H2O.7, H2O.7, H2O.7, H2O.11 MG.10: 1 residues within 4Å: Chain B: K.149 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:K.149, H2O.7, H2O.9, H2O.12 MG.20: 3 residues within 4Å: Chain D: S.34, D.57 Ligands: ADP.19 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.34, H2O.20, H2O.20, H2O.20, H2O.24 MG.21: 1 residues within 4Å: Chain D: K.149 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:K.149, H2O.20, H2O.22, H2O.25

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
A

B
B

D
B

Probable hydrogenase nickel incorporation protein HypA

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

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