SMTL ID : 3wjp.1

Crystal structure of the HypE CA form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 22 residues within 4Å: Chain A: M.16, L.20, I.24, L.38, L.41, D.42, D.43, D.59, D.84, T.223, R.224, C.338 Chain B: N.97, M.99, T.130, G.131, D.132, T.133, K.134 Ligands: MG.2, MG.3, MG.4 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:N.97, B:T.130, B:G.131, B:D.132, B:T.133, B:T.133, A:L.41, A:T.223, A:R.224, A:R.224, A:R.224 Water bridges: B:T.133, B:T.133, B:K.134, A:D.42, A:T.223, A:T.223, A:R.224 Salt bridges: A:R.224 ANP.18: 22 residues within 4Å: Chain A: N.97, M.99, T.130, G.131, D.132, T.133, K.134 Chain B: M.16, L.20, I.24, L.38, L.41, D.42, D.43, D.59, D.84, T.223, R.224, C.338 Ligands: MG.19, MG.20, MG.21 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:N.97, A:T.130, A:T.130, A:G.131, A:T.133, B:L.41, B:D.43, B:T.223, B:R.224, B:R.224, B:R.224 Water bridges: A:T.133, A:T.133, A:K.134, B:D.42, B:T.223, B:T.223, B:R.224 Salt bridges: B:R.224

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.59, R.224 Chain B: D.132 Ligands: ANP.1, MG.3 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.59, B:D.132, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.59, D.84 Ligands: ANP.1, MG.2, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:D.84, H2O.1, H2O.7 MG.4: 5 residues within 4Å: Chain A: D.43, D.84, D.221 Ligands: ANP.1, MG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.43, A:D.84, A:D.221, H2O.1, H2O.1 MG.19: 5 residues within 4Å: Chain A: D.132 Chain B: D.59, R.224 Ligands: ANP.18, MG.20 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.132, B:D.59, H2O.14 MG.20: 5 residues within 4Å: Chain B: D.59, D.84 Ligands: ANP.18, MG.19, MG.21 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:D.84, H2O.14, H2O.20 MG.21: 5 residues within 4Å: Chain B: D.43, D.84, D.221 Ligands: ANP.18, MG.20 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.43, B:D.84, B:D.221, H2O.14, H2O.14

4 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.5: 4 residues within 4Å: Chain A: F.189, E.190, P.253, E.254 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.189, A:P.253 Hydrogen bonds: A:E.190, A:E.254 BEN.6: 4 residues within 4Å: Chain A: I.47, P.48, F.49 Chain B: I.93 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.47, A:F.49, B:I.93 BEN.22: 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 Hydrogen bonds: B:E.190, B:E.254, B:E.254 Water bridges: B:E.190 BEN.23: 4 residues within 4Å: Chain A: I.93 Chain B: I.47, P.48, F.49 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.93, B:I.47, B:F.49

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

SO4.7: 3 residues within 4Å: Chain A: R.252, R.298, N.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.299 Water bridges: A:R.252 Salt bridges: A:R.252, A:R.298 SO4.8: 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 SO4.9: 2 residues within 4Å: Chain A: P.69, G.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.70 SO4.10: 1 residues within 4Å: Chain A: R.292 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.292 Salt bridges: A:R.292 SO4.11: 1 residues within 4Å: Chain A: R.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.122 Salt bridges: A:R.122 SO4.24: 3 residues within 4Å: Chain B: R.252, R.298, N.299 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.299 Water bridges: B:R.252 Salt bridges: B:R.252, B:R.298 SO4.25: 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 SO4.26: 2 residues within 4Å: Chain B: P.69, G.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.70 SO4.27: 1 residues within 4Å: Chain B: R.292 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.292 Salt bridges: B:R.292 SO4.28: 1 residues within 4Å: Chain B: R.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.122 Salt bridges: B:R.122

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain A: T.172, D.175, K.194, S.195, D.196, R.252, K.274 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.194, A:R.252, A:K.274, A:K.274 Water bridges: A:S.195 GOL.13: 5 residues within 4Å: Chain A: K.64, R.184, P.335 Chain B: E.137 Ligands: GOL.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.184, B:E.137 Water bridges: A:R.184 GOL.14: 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:S.32, A:G.37 Water bridges: A:D.39 GOL.15: 4 residues within 4Å: Chain A: K.64, P.65, R.184 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.184 GOL.29: 7 residues within 4Å: Chain B: T.172, D.175, K.194, S.195, D.196, R.252, K.274 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.194, B:R.252, B:K.274, B:K.274 Water bridges: B:S.195 GOL.30: 5 residues within 4Å: Chain A: E.137 Chain B: K.64, R.184, P.335 Ligands: GOL.32 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.137, B:R.184 Water bridges: A:E.137, B:R.184 GOL.31: 6 residues within 4Å: Chain B: S.32, G.35, I.36, G.37, D.39, A.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.32, B:G.37 Water bridges: B:D.39 GOL.32: 4 residues within 4Å: Chain B: K.64, P.65, R.184 Ligands: GOL.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.184

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

PGE.16: 7 residues within 4Å: Chain A: G.89, E.91, I.151, A.152, E.153, A.208, W.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.89, A:E.153 Water bridges: A:H.154 PGE.17: 7 residues within 4Å: Chain A: R.256, S.259, E.260, I.264, S.265, P.266, Y.267 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.265, A:S.265, A:Y.267 PGE.33: 7 residues within 4Å: Chain B: G.89, E.91, I.151, A.152, E.153, A.208, W.213 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.89, B:E.153, B:E.153 Water bridges: B:H.154 PGE.34: 7 residues within 4Å: Chain B: R.256, S.259, E.260, I.264, S.265, P.266, Y.267 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.265, B:S.265

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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