SMTL ID : 7lv1.1

Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in the presence of Cu(II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 19 residues within 4Å: Chain A: L.3, E.4, M.7, E.8, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 Ligands: CA.3 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:N.11, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:L.68, A:R.106 Hydrogen bonds: A:E.4, A:E.8 Water bridges: A:R.106, A:R.106 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.4: 19 residues within 4Å: Chain B: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, H.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:L.10, B:L.10, 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 Metal complexes: B:H.102

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 1 residues within 4Å: Chain A: D.66 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: E.4 Ligands: HEC.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.4, H2O.2 CA.6: 2 residues within 4Å: Chain B: K.19, D.21 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:K.19, B:D.21, B:D.21, H2O.4, H2O.5 CA.7: 3 residues within 4Å: Chain B: L.38, Q.41, K.42 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.38, H2O.7

1 x CU: COPPER (II) ION(Non-covalent)

CU.5: 5 residues within 4Å: Chain A: H.67, H.71 Chain B: H.67, H.71, H.97 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.67, A:H.71, B:H.67, B:H.71, B:H.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, T.S. et al., Structure-guided metal selectivity in malleable protein interfacemediated by single disulfide bond. To Be Published

Release Date

2022-03-02

Peptides

Soluble cytochrome b562: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

Soluble cytochrome b562

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