SMTL ID : 3wjr.1

crystal structure of HypE in complex with a nucleotide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

4 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.1: 4 residues within 4Å: Chain A: F.189, E.190, P.253, E.254 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.189, A:P.253, A:E.254 Hydrogen bonds: A:E.190, A:E.254 BEN.2: 5 residues within 4Å: Chain A: I.47, P.48, F.49 Chain B: E.91, I.93 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.91 Hydrophobic interactions: A:I.47, A:F.49, A:F.49 BEN.13: 4 residues within 4Å: Chain B: F.189, E.190, P.253, E.254 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.189, B:P.253, B:E.254 Hydrogen bonds: B:E.190, B:E.254, B:E.254 BEN.14: 5 residues within 4Å: Chain A: E.91, I.93 Chain B: I.47, P.48, F.49 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.91 Hydrophobic interactions: B:I.47, B:F.49, B:F.49

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 13 residues within 4Å: Chain A: M.16, L.20, I.24, L.38, L.41, D.42, R.224 Chain B: N.97, M.99, T.130, G.131, D.132, T.133 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:L.41, B:N.97, B:T.130, B:G.131, B:D.132, B:T.133, B:T.133 Water bridges: A:D.42, A:R.224, B:T.133 Salt bridges: A:R.224 AMP.15: 13 residues within 4Å: Chain A: N.97, M.99, T.130, G.131, D.132, T.133 Chain B: M.16, L.20, I.24, L.38, L.41, D.42, R.224 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.97, A:T.130, A:T.130, A:G.131, A:T.133, B:L.41 Water bridges: A:T.133, B:D.42, B:R.224 Salt bridges: B:R.224

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: F.68, P.69, G.70, G.71, K.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.70 Water bridges: A:F.68, A:G.71 SO4.5: 3 residues within 4Å: Chain A: R.252, R.298, N.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.299 Salt bridges: A:R.252, A:R.298 SO4.6: 3 residues within 4Å: Chain A: D.309, Y.310, R.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.310, A:R.311 Salt bridges: A:R.311 SO4.7: 1 residues within 4Å: Chain A: R.292 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.292 SO4.8: 1 residues within 4Å: Chain A: R.122 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.122 SO4.16: 5 residues within 4Å: Chain B: F.68, P.69, G.70, G.71, K.194 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.70 Water bridges: B:F.68, B:G.71 SO4.17: 3 residues within 4Å: Chain B: R.252, R.298, N.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.299 Salt bridges: B:R.252, B:R.298 SO4.18: 3 residues within 4Å: Chain B: D.309, Y.310, R.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.310, B:R.311 Salt bridges: B:R.311 SO4.19: 1 residues within 4Å: Chain B: R.292 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.292 SO4.20: 1 residues within 4Å: Chain B: R.122 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.122

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 9 residues within 4Å: Chain A: G.89, E.91, I.151, A.152, E.153, W.201, A.208, E.209, W.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.89, A:E.153 Water bridges: A:H.154 PGE.21: 9 residues within 4Å: Chain B: G.89, E.91, I.151, A.152, E.153, W.201, A.208, E.209, W.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.89, B:E.153 Water bridges: B:H.154

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: S.32, G.35, I.36, G.37, D.39, A.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.37 Water bridges: A:S.32, A:S.32 GOL.22: 6 residues within 4Å: Chain B: S.32, G.35, I.36, G.37, D.39, A.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.37, B:D.39 Water bridges: B:S.32, B:S.32

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 8 residues within 4Å: Chain A: I.251, R.256, S.259, E.260, I.264, S.265, P.266, Y.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.259, A:E.260, A:I.264, A:Y.267 PEG.23: 8 residues within 4Å: Chain B: I.251, R.256, S.259, E.260, I.264, S.265, P.266, Y.267 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.259, B:I.264, B:Y.267

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain A: D.43, D.84, D.221 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.43, A:D.84, H2O.6 MG.24: 3 residues within 4Å: Chain B: D.43, D.84, D.221 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.43, B:D.84, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tominaga, T. et al., Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-12-18

Peptides

Hydrogenase expression/formation protein HypE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hydrogenase expression/formation protein HypE

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