SMTL ID : 8zxr.2 (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-6-6-mer

Ligands

6 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) NI.16: 11 residues within 4Å: Chain G: H.17 Chain I: H.17 Chain K: H.17 Ligands: CL.17, CL.18, NI.21, CL.22, CL.23, NI.26, CL.27, CL.28 No protein-ligand interaction detected (PLIP) NI.21: 11 residues within 4Å: Chain G: H.17 Chain I: H.17 Chain K: H.17 Ligands: NI.16, CL.17, CL.18, CL.22, CL.23, NI.26, CL.27, CL.28 No protein-ligand interaction detected (PLIP) NI.26: 11 residues within 4Å: Chain G: H.17 Chain I: H.17 Chain K: H.17 Ligands: NI.16, CL.17, CL.18, NI.21, CL.22, CL.23, CL.27, CL.28 No protein-ligand interaction detected (PLIP)

12 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 CL.17: 11 residues within 4Å: Chain I: R.13, H.17 Chain K: R.13 Ligands: NI.16, CL.18, NI.21, CL.22, CL.23, NI.26, CL.27, CL.28 Ligand excluded by PLIP CL.18: 12 residues within 4Å: Chain G: H.17 Chain K: H.17 Ligands: NI.16, CL.17, HEC.19, NI.21, CL.22, CL.23, NI.26, CL.27, CL.28, HEC.29 Ligand excluded by PLIP CL.22: 11 residues within 4Å: Chain G: R.13 Chain K: R.13, H.17 Ligands: NI.16, CL.17, CL.18, NI.21, CL.23, NI.26, CL.27, CL.28 Ligand excluded by PLIP CL.23: 12 residues within 4Å: Chain G: H.17 Chain I: H.17 Ligands: NI.16, CL.17, CL.18, HEC.19, NI.21, CL.22, HEC.24, NI.26, CL.27, CL.28 Ligand excluded by PLIP CL.27: 11 residues within 4Å: Chain G: R.13, H.17 Chain I: R.13 Ligands: NI.16, CL.17, CL.18, NI.21, CL.22, CL.23, NI.26, CL.28 Ligand excluded by PLIP CL.28: 12 residues within 4Å: Chain I: H.17 Chain K: H.17 Ligands: NI.16, CL.17, CL.18, NI.21, CL.22, CL.23, HEC.24, NI.26, CL.27, HEC.29 Ligand excluded by PLIP

6 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: 7 interactions with chain A, 2 interactions with chain E, 2 interactions with chain B, 3 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: A:A.25, A:I.84, A:A.87, B:Q.2, D:V.10, D:V.10 Salt bridges: A:R.13, A:H.17, A:H.17, E:H.17, D:H.8, C:H.80 Metal complexes: A:H.22, B:H.8 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: 1 interactions with chain E, 2 interactions with chain D, 3 interactions with chain F, 2 interactions with chain A, 7 interactions with chain C, Salt bridges: E:H.80, F:H.8, A:H.17, C:R.13, C:H.17, C:H.17 Hydrophobic interactions: D:Q.2, F:V.10, F:V.10, C:A.25, C:I.84, C:A.87 Metal complexes: D:H.8, C:H.22 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: 7 interactions with chain E, 3 interactions with chain B, 1 interactions with chain A, 2 interactions with chain F, 2 interactions with chain C, Hydrophobic interactions: E:A.25, E:I.84, E:A.87, B:V.10, B:V.10, F:Q.2 Salt bridges: E:R.13, E:H.17, E:H.17, B:H.8, A:H.80, C:H.17 Metal complexes: E:H.22, F:H.8 Water bridges: C:H.17 HEC.19: 27 residues within 4Å: Chain G: 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 H: Q.2, K.3, C.4, C.7, H.8 Chain I: H.80 Chain J: Q.6, C.7, H.8, V.10 Chain K: H.17 Ligands: CL.18, CL.23, HEC.24, HEC.29 16 PLIP interactions: 2 interactions with chain H, 8 interactions with chain G, 3 interactions with chain J, 2 interactions with chain K, 1 interactions with chain I, Hydrophobic interactions: H:Q.2, G:A.25, G:I.84, G:A.87, J:V.10, J:V.10 Metal complexes: H:H.8, G:H.22 Hydrogen bonds: G:D.21 Salt bridges: G:R.13, G:H.17, G:H.17, J:H.8, K:H.17, I:H.80 Water bridges: K:H.17 HEC.24: 27 residues within 4Å: Chain G: H.17 Chain I: 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 J: Q.2, K.3, C.4, C.7, H.8 Chain K: H.80 Chain L: Q.6, C.7, H.8, V.10 Ligands: HEC.19, CL.23, CL.28, HEC.29 16 PLIP interactions: 8 interactions with chain I, 2 interactions with chain J, 3 interactions with chain L, 1 interactions with chain K, 2 interactions with chain G, Hydrophobic interactions: I:A.25, I:I.84, I:A.87, J:Q.2, L:V.10, L:V.10 Hydrogen bonds: I:D.21 Salt bridges: I:R.13, I:H.17, I:H.17, L:H.8, K:H.80, G:H.17 Metal complexes: I:H.22, J:H.8 Water bridges: G:H.17 HEC.29: 27 residues within 4Å: Chain G: H.80 Chain H: Q.6, C.7, H.8, V.10 Chain I: H.17 Chain K: 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 L: Q.2, K.3, C.4, C.7, H.8 Ligands: CL.18, HEC.19, HEC.24, CL.28 16 PLIP interactions: 3 interactions with chain H, 2 interactions with chain I, 8 interactions with chain K, 2 interactions with chain L, 1 interactions with chain G, Hydrophobic interactions: H:V.10, H:V.10, K:A.25, K:I.84, K:A.87, L:Q.2 Salt bridges: H:H.8, I:H.17, K:R.13, K:H.17, K:H.17, G:H.80 Water bridges: I:H.17 Hydrogen bonds: K:D.21 Metal complexes: K:H.22, L:H.8

6 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 D, 2 interactions with chain B Hydrogen bonds: D:Q.6, D:Q.11, B:Q.2, B:Q.2 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 GOL.20: 5 residues within 4Å: Chain H: A.5, Q.6, T.9, Q.11 Chain L: Q.2 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain L Hydrogen bonds: H:Q.6, H:Q.11, L:Q.2, L:Q.2 GOL.25: 5 residues within 4Å: Chain H: Q.2 Chain J: A.5, Q.6, T.9, Q.11 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain H Hydrogen bonds: J:Q.6, J:Q.11, H:Q.2, H:Q.2 GOL.30: 5 residues within 4Å: Chain J: Q.2 Chain L: A.5, Q.6, T.9, Q.11 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain L Hydrogen bonds: J:Q.2, J:Q.2, L:Q.6, L:Q.11

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: ACEGIK
Cytochrome c: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

B
B

D
B

F
B

H
B

J
B

L
B

Ssr1698 protein

Cytochrome c

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