SMTL ID : 3wve.1

Crystal structure of Nitrile Hydratase mutant bR56K complexed with Trimethylacetonitrile, before photo-activation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

hetero-oligomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: C.110, C.113, S.114, C.115 Ligands: NO.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.110, NO.2

1 x NO: NITRIC OXIDE(Non-covalent)

NO.2: 5 residues within 4Å: Chain A: C.113, S.114, C.115 Ligands: FE.1, TAN.7 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.91, A:T.116, A:T.116, A:W.118

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: T.126, W.127 Chain B: I.24 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: R.55, T.192, K.193 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: S.20, W.24 Chain B: E.31, W.32 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: T.121, R.132, L.208, E.209, P.210 Ligand excluded by PLIP

1 x TAN: 2,2-DIMETHYLPROPANENITRILE(Non-covalent)

TAN.7: 8 residues within 4Å: Chain B: Y.37, M.40, V.52, V.55, K.56, Y.72, Y.76 Ligands: NO.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.37, B:K.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamanaka, Y. et al., Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-06-17

Peptides

Nitrile hydratase subunit alpha: A
Nitrile hydratase subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitrile hydratase subunit alpha

Nitrile hydratase subunit beta

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