SMTL ID : 8drd.1

Ni(II)-bound B2 dimer (H60/H100/H104)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 17 residues within 4Å: Chain A: E.4, M.7, L.10, N.11, M.33, P.45, P.46, K.47, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:N.11, A:P.45, A:F.61, A:F.61, A:F.65, A:F.65, A:F.65, A:L.68, A:Y.105 Hydrogen bonds: A:E.4 Salt bridges: A:K.47 Metal complexes: A:H.102 HEC.4: 16 residues within 4Å: Chain B: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, C.98, C.101, H.102, R.106 Ligands: MPD.3 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.14, B:P.45, B:F.65, B:F.65, B:F.65, B:R.106, B:R.106 Hydrogen bonds: B:E.4 Water bridges: B:L.3, B:R.106, B:R.106 pi-Stacking: B:H.102 Metal complexes: B:H.102

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

NI.2: 4 residues within 4Å: Chain A: H.60, H.104 Chain B: H.100, H.104 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.100, B:H.104, A:H.60, A:H.104, H2O.2, H2O.3 NI.5: 1 residues within 4Å: Chain B: D.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.2

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 9 residues within 4Å: Chain A: Q.103, H.104 Chain B: H.60, G.64, T.97, H.100, C.101, H.104 Ligands: HEC.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, T.S. et al., Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. J.Am.Chem.Soc. (2022)

Release Date

2022-10-12

Peptides

Soluble cytochrome b562: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Soluble cytochrome b562

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