SMTL ID : 7vos.1

High-resolution neutron and X-ray joint refined structure of high-potential iron-sulfur protein in the oxidized state

Coordinates

PDB Format

Method

NEUTRON DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 13 residues within 4Å: Chain A: Y.19, C.43, C.46, F.48, M.49, C.61, L.63, F.64, I.69, W.74, C.75, S.77, W.78 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.43, A:C.46, A:C.61, A:C.75

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: A.6, V.7, T.8, D.11, K.67 Ligands: NH4.14 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.6, A:T.8, A:T.8, A:D.11, A:D.11 Salt bridges: A:K.67 SO4.3: 2 residues within 4Å: Chain A: A.1, A.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.2 Water bridges: A:A.2, A:A.2, A:Q.21 SO4.4: 3 residues within 4Å: Chain A: H.42, A.44 Ligands: NH4.15 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.42 SO4.5: 4 residues within 4Å: Chain A: G.54, E.55, G.56, K.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.55, A:E.55, A:G.56 Salt bridges: A:K.59 SO4.6: 6 residues within 4Å: Chain A: M.49, Q.50, A.51, N.52, V.53 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.51, A:N.52

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: I.15, K.18, E.27 Ligands: NH4.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.18, A:E.27 GOL.8: 6 residues within 4Å: Chain A: Q.50, N.52, V.53 Ligands: SO4.6, GOL.9, D3O.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.50 GOL.9: 5 residues within 4Å: Chain A: Q.47, F.48, Q.50, Q.62 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.47, A:Q.50 GOL.10: 3 residues within 4Å: Chain A: P.37, E.39, E.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:E.39 GOL.11: 4 residues within 4Å: Chain A: L.17, R.33, A.76, S.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.33, A:A.76, A:S.77

4 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.12: 8 residues within 4Å: Chain A: Q.50, G.60, C.61, Q.62, F.64, P.65, G.66, K.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.50, A:Q.50, A:G.66 Water bridges: A:C.61 NH4.13: 3 residues within 4Å: Chain A: K.18, E.27 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.18, A:E.27 NH4.14: 7 residues within 4Å: Chain A: P.3, A.4, N.5, A.6, V.7, T.8 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.5, A:A.6, A:A.6 NH4.15: 1 residues within 4Å: Ligands: SO4.4 No protein-ligand interaction detected (PLIP)

1 x D3O: trideuteriooxidanium(Non-functional Binders)

D3O.16: 1 residues within 4Å: Ligands: GOL.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanazono, Y. et al., Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis. Sci Adv (2022)

Release Date

2022-06-01

Peptides

High-potential iron-sulfur protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

High-potential iron-sulfur protein

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