SMTL ID : 6dhy.1

Crystallogrpahic tetramer of Zn-bound RIDC1 variant bearing two disulfide bonded cysteines

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 15 residues within 4Å: Chain A: E.4, M.7, L.10, N.11, M.33, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:N.11, A:F.61, A:F.65, A:F.65, A:L.68, A:R.106 Hydrogen bonds: A:E.4 pi-Stacking: A:H.102, A:H.102 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.5: 15 residues within 4Å: Chain B: E.4, M.7, L.10, N.11, L.14, M.33, P.46, F.61, F.65, L.94, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:E.4, B:M.7, B:L.10, B:F.61, B:F.65, B:F.65, B:L.94, B:R.106, B:R.106 Hydrogen bonds: B:E.4 pi-Stacking: B:H.102 Metal complexes: B:H.102 HEC.7: 21 residues within 4Å: Chain C: L.3, E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 Ligands: CA.8 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.3, C:E.4, C:M.7, C:L.10, C:N.11, C:L.14, C:P.45, C:F.65, C:F.65, C:L.68, C:L.94, C:T.97, C:R.106 pi-Stacking: C:H.102, C:H.102 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEC.15: 17 residues within 4Å: Chain D: L.3, E.4, M.7, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:L.3, D:M.7, D:L.14, D:P.45, D:F.65, D:F.65, D:F.65, D:L.68, D:R.106 pi-Stacking: D:H.102, D:H.102 Metal complexes: D:H.102

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.2, D.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.2 CA.8: 2 residues within 4Å: Chain C: E.4 Ligands: HEC.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.4 CA.9: 2 residues within 4Å: Chain C: D.5 Ligands: ZN.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.5

10 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.3: 4 residues within 4Å: Chain A: H.73, H.77 Chain C: D.74 Chain D: H.63 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 interactions with chain C Metal complexes: D:H.63, A:H.73, A:H.77, C:D.74 ZN.4: 2 residues within 4Å: Chain A: A.1, D.39 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.1, A:D.39 ZN.6: 4 residues within 4Å: Chain B: H.73, H.77 Chain C: H.63 Chain D: D.74 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 interactions with chain D Metal complexes: B:H.73, B:H.77, C:H.63, D:D.74, D:D.74 ZN.10: 5 residues within 4Å: Chain A: D.74 Chain B: H.63, I.67 Chain C: H.73, H.77 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.74, A:D.74, C:H.73, C:H.77, B:H.63 ZN.11: 2 residues within 4Å: Chain C: E.8, D.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.8, C:D.12, C:D.12 ZN.12: 4 residues within 4Å: Chain C: D.5 Ligands: CA.9, ZN.13, ZN.14 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.5, C:D.5 ZN.13: 2 residues within 4Å: Ligands: ZN.12, ZN.14 No protein-ligand interaction detected (PLIP) ZN.14: 4 residues within 4Å: Chain C: D.2, D.5 Ligands: ZN.12, ZN.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.5 ZN.16: 4 residues within 4Å: Chain A: H.63 Chain B: D.74 Chain D: H.73, H.77 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 interactions with chain A Metal complexes: B:D.74, B:D.74, D:H.73, D:H.77, A:H.63 ZN.17: 2 residues within 4Å: Chain D: D.2, D.5 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.5, D:D.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Churchfield, L.A. et al., Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. J. Am. Chem. Soc. (2018)

Release Date

2018-07-25

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Soluble cytochrome b562

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