SMTL ID : 6dhz.1

Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide bonded cysteines

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-octamer

Ligands

8 x HEC: HEME C(Covalent)

HEC.1: 17 residues within 4Å: Chain A: L.3, E.4, M.7, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:L.3, A:M.7, A:N.11, A:P.45, A:F.65, A:F.65, A:F.65, A:T.97, A:R.106 Hydrogen bonds: A:E.4 pi-Stacking: A:H.102, A:H.102 Metal complexes: A:H.102 HEC.4: 17 residues within 4Å: Chain B: E.4, M.7, L.10, N.11, L.14, P.45, P.46, F.61, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 Ligands: CA.5 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:R.106 Hydrogen bonds: B:E.4, B:E.8 pi-Stacking: B:H.102, B:H.102 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.7: 14 residues within 4Å: Chain C: L.3, E.4, M.7, L.10, N.11, L.14, M.33, F.61, F.65, T.97, C.98, C.101, H.102, R.106 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:L.3, C:M.7, C:N.11, C:L.14, C:F.65, C:F.65 Hydrogen bonds: C:E.4, C:E.4 pi-Stacking: C:H.102, C:H.102 pi-Cation interactions: C:H.102, C:H.102 Metal complexes: C:H.102 HEC.10: 15 residues within 4Å: Chain D: L.3, E.4, M.7, E.8, N.11, L.14, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:L.3, D:M.7, D:N.11, D:F.65, D:F.65, D:F.65 Hydrogen bonds: D:E.8 pi-Stacking: D:H.102 pi-Cation interactions: D:R.106 Metal complexes: D:H.102 HEC.12: 17 residues within 4Å: Chain E: L.3, E.4, M.7, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:L.3, E:M.7, E:N.11, E:P.45, E:F.65, E:F.65, E:F.65, E:T.97, E:R.106 Hydrogen bonds: E:E.4, E:E.4 pi-Stacking: E:H.102, E:H.102 Metal complexes: E:H.102 HEC.15: 17 residues within 4Å: Chain F: E.4, M.7, L.10, N.11, L.14, P.45, P.46, F.61, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 Ligands: CA.16 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:M.7, F:L.10, F:P.45, F:F.61, F:F.65, F:F.65, F:F.65, F:L.68, F:R.106 Hydrogen bonds: F:E.8 pi-Stacking: F:H.102, F:H.102 pi-Cation interactions: F:R.106 Metal complexes: F:H.102 HEC.18: 14 residues within 4Å: Chain G: L.3, E.4, M.7, L.10, N.11, L.14, M.33, F.61, F.65, T.97, C.98, C.101, H.102, R.106 12 PLIP interactions: 12 interactions with chain G, Hydrophobic interactions: G:L.3, G:M.7, G:N.11, G:L.14, G:F.65, G:F.65 Hydrogen bonds: G:E.4 pi-Stacking: G:H.102, G:H.102 pi-Cation interactions: G:H.102, G:H.102 Metal complexes: G:H.102 HEC.21: 15 residues within 4Å: Chain H: L.3, E.4, M.7, E.8, N.11, L.14, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain H, Hydrophobic interactions: H:L.3, H:M.7, H:N.11, H:F.65, H:F.65, H:F.65 Hydrogen bonds: H:E.4 pi-Stacking: H:H.102 pi-Cation interactions: H:R.106 Metal complexes: H:H.102

14 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: K.19, D.21 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: D.2, D.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.2, A:D.5 CA.5: 2 residues within 4Å: Chain B: E.4 Ligands: HEC.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.4 CA.6: 2 residues within 4Å: Chain B: A.1, D.39 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.1, B:D.39, B:D.39 CA.8: 1 residues within 4Å: Chain C: D.21 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain C: D.5, E.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.5, C:E.8 CA.11: 2 residues within 4Å: Chain D: A.1, D.39 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.39 CA.13: 2 residues within 4Å: Chain E: K.19, D.21 No protein-ligand interaction detected (PLIP) CA.14: 2 residues within 4Å: Chain E: D.2, D.5 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.2, E:D.5 CA.16: 2 residues within 4Å: Chain F: E.4 Ligands: HEC.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.4 CA.17: 2 residues within 4Å: Chain F: A.1, D.39 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:A.1, F:D.39, F:D.39 CA.19: 1 residues within 4Å: Chain G: D.21 No protein-ligand interaction detected (PLIP) CA.20: 2 residues within 4Å: Chain G: D.5, E.8 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.5, G:E.8 CA.22: 2 residues within 4Å: Chain H: A.1, D.39 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.39

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Soluble cytochrome b562

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