SMTL ID : 7lsj.1

Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A, crystallized in the presence of Cu(II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 18 residues within 4Å: Chain A: 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, C.98, C.101, H.102, Y.105, R.106 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.3, A:M.7, A:L.10, A:N.11, A:L.14, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:R.106 Hydrogen bonds: A:E.4 Water bridges: A:E.8, A:R.106, A:R.106 pi-Stacking: A:H.102 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 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:P.45, B:F.65, B:F.65, B:F.65, B:R.106 Hydrogen bonds: B:E.4 Water bridges: B:E.4, B:R.106 pi-Cation interactions: B:R.106 Metal complexes: B:H.102

5 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 1 residues within 4Å: Chain A: D.66 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.66, A:D.66 CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Chain B: E.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.4, H2O.9, H2O.10, H2O.10, H2O.10 CA.7: 1 residues within 4Å: Chain B: D.50 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.50 CA.8: 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.13

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: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.67, B:H.71, B:H.97, A:H.67, A:H.71

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

2022-02-23

Peptides

Soluble cytochrome b562: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

Soluble cytochrome b562

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