SMTL ID : 8zxr.3 (3 other biounits)

Crystal structure of Ssr1698 in complex with heme c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-3-3-mer

Ligands

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

NI.1: 11 residues within 4Å: Chain A: H.17 Chain C: H.17 Chain E: H.17 Ligands: CL.2, CL.3, NI.6, CL.7, CL.8, NI.11, CL.12, CL.13 No protein-ligand interaction detected (PLIP) NI.6: 11 residues within 4Å: Chain A: H.17 Chain C: H.17 Chain E: H.17 Ligands: NI.1, CL.2, CL.3, CL.7, CL.8, NI.11, CL.12, CL.13 No protein-ligand interaction detected (PLIP) NI.11: 11 residues within 4Å: Chain A: H.17 Chain C: H.17 Chain E: H.17 Ligands: NI.1, CL.2, CL.3, NI.6, CL.7, CL.8, CL.12, CL.13 No protein-ligand interaction detected (PLIP)

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 11 residues within 4Å: Chain C: R.13, H.17 Chain E: R.13 Ligands: NI.1, CL.3, NI.6, CL.7, CL.8, NI.11, CL.12, CL.13 Ligand excluded by PLIP CL.3: 12 residues within 4Å: Chain A: H.17 Chain E: H.17 Ligands: NI.1, CL.2, HEC.4, NI.6, CL.7, CL.8, NI.11, CL.12, CL.13, HEC.14 Ligand excluded by PLIP CL.7: 11 residues within 4Å: Chain A: R.13 Chain E: R.13, H.17 Ligands: NI.1, CL.2, CL.3, NI.6, CL.8, NI.11, CL.12, CL.13 Ligand excluded by PLIP CL.8: 12 residues within 4Å: Chain A: H.17 Chain C: H.17 Ligands: NI.1, CL.2, CL.3, HEC.4, NI.6, CL.7, HEC.9, NI.11, CL.12, CL.13 Ligand excluded by PLIP CL.12: 11 residues within 4Å: Chain A: R.13, H.17 Chain C: R.13 Ligands: NI.1, CL.2, CL.3, NI.6, CL.7, CL.8, NI.11, CL.13 Ligand excluded by PLIP CL.13: 12 residues within 4Å: Chain C: H.17 Chain E: H.17 Ligands: NI.1, CL.2, CL.3, NI.6, CL.7, CL.8, HEC.9, NI.11, CL.12, HEC.14 Ligand excluded by PLIP

3 x HEC: HEME C(Covalent)

HEC.4: 27 residues within 4Å: Chain A: R.13, I.14, H.17, M.18, D.21, H.22, A.25, Y.29, H.80, L.83, I.84, A.87 Chain B: Q.2, K.3, C.4, C.7, H.8 Chain C: H.80 Chain D: Q.6, C.7, H.8, V.10 Chain E: H.17 Ligands: CL.3, CL.8, HEC.9, HEC.14 15 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A, 3 interactions with chain D, 2 interactions with chain E, 1 interactions with chain C, Hydrophobic interactions: B:Q.2, A:A.25, A:I.84, A:A.87, D:V.10, D:V.10 Metal complexes: B:H.8, A:H.22 Salt bridges: A:R.13, A:H.17, A:H.17, D:H.8, E:H.17, C:H.80 Water bridges: E:H.17 HEC.9: 27 residues within 4Å: Chain A: H.17 Chain C: R.13, I.14, H.17, M.18, D.21, H.22, A.25, Y.29, H.80, L.83, I.84, A.87 Chain D: Q.2, K.3, C.4, C.7, H.8 Chain E: H.80 Chain F: Q.6, C.7, H.8, V.10 Ligands: HEC.4, CL.8, CL.13, HEC.14 15 PLIP interactions: 3 interactions with chain F, 7 interactions with chain C, 2 interactions with chain D, 2 interactions with chain A, 1 interactions with chain E, Hydrophobic interactions: F:V.10, F:V.10, C:A.25, C:I.84, C:A.87, D:Q.2 Salt bridges: F:H.8, C:R.13, C:H.17, C:H.17, A:H.17, E:H.80 Metal complexes: C:H.22, D:H.8 Water bridges: A:H.17 HEC.14: 27 residues within 4Å: Chain A: H.80 Chain B: Q.6, C.7, H.8, V.10 Chain C: H.17 Chain E: R.13, I.14, H.17, M.18, D.21, H.22, A.25, Y.29, H.80, L.83, I.84, A.87 Chain F: Q.2, K.3, C.4, C.7, H.8 Ligands: CL.3, HEC.4, HEC.9, CL.13 15 PLIP interactions: 3 interactions with chain B, 7 interactions with chain E, 2 interactions with chain C, 2 interactions with chain F, 1 interactions with chain A, Hydrophobic interactions: B:V.10, B:V.10, E:A.25, E:I.84, E:A.87, F:Q.2 Salt bridges: B:H.8, E:R.13, E:H.17, E:H.17, C:H.17, A:H.80 Metal complexes: E:H.22, F:H.8 Water bridges: C:H.17

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: A.5, Q.6, T.9, Q.11 Chain F: Q.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:Q.6, B:Q.11, F:Q.2, F:Q.2 GOL.10: 5 residues within 4Å: Chain B: Q.2 Chain D: A.5, Q.6, T.9, Q.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.2, B:Q.2, D:Q.6, D:Q.11 GOL.15: 5 residues within 4Å: Chain D: Q.2 Chain F: A.5, Q.6, T.9, Q.11 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:Q.6, F:Q.11, D:Q.2, D:Q.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X.Y. et al., Structural Basis for Monomer-Dimer Transition of Dri1 Upon Heme Binding. Proteins (2025)

Release Date

2024-12-25

Peptides

Ssr1698 protein: ACE
Cytochrome c: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Ssr1698 protein

Cytochrome c

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