SMTL ID : 5vp3.1

Light-sensitive photoprotein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 6 residues within 4Å: Chain A: D.44, D.46, D.48, K.50, M.51, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.44, A:D.48, A:K.50, A:E.55, H2O.1 CD.2: 7 residues within 4Å: Chain A: D.136, D.138, D.140, T.142, V.143, D.144, E.147 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.136, A:D.140, A:T.142, A:E.147, H2O.1 CD.3: 7 residues within 4Å: Chain A: D.170, D.172, T.174, K.176, L.177, E.178, E.181 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.170, A:T.174, A:K.176, A:E.178, A:E.181 CD.4: 3 residues within 4Å: Chain A: R.187, K.188, E.192 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.192, A:E.192, H2O.4, H2O.4

1 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 1 residues within 4Å: Chain A: H.184 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.184, H2O.4

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.6: 7 residues within 4Å: Chain A: A.69, Q.73, D.133, V.134, D.136, D.137, G.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Molakarimi, M. et al., Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations. J. Biol. Chem. (2019)

Release Date

2018-05-09

Peptides

Mnemiopsin 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mnemiopsin 1