SMTL ID : 6a6f.1

Crystal structure of Putative iron-sulfur cluster assembly scaffold protein for SUF system (FiSufU) from thermophilic Fervidobacterium Islandicum AW-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: E.92, K.129, E.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.129, A:E.132 GOL.2: 4 residues within 4Å: Chain A: E.8, F.9, D.12, Y.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.12 Water bridges: A:Y.13 GOL.10: 4 residues within 4Å: Chain B: D.50, T.80, K.81, Q.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.80, B:Q.82 GOL.11: 4 residues within 4Å: Chain B: D.12, Y.13, L.16, E.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.74 Water bridges: B:D.12 GOL.12: 2 residues within 4Å: Chain A: S.2 Chain B: E.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.2, A:S.2

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: P.118, V.121, K.122, L.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.118 PEG.4: 2 residues within 4Å: Chain A: K.22, E.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:K.22 PEG.13: 6 residues within 4Å: Chain B: K.89, N.90, E.99, F.100, D.101 Ligands: PEG.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.89, B:K.89 Water bridges: B:N.90, B:E.99, B:E.102 PEG.14: 2 residues within 4Å: Chain B: E.99 Ligands: PEG.13 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.102 PEG.15: 1 residues within 4Å: Chain B: D.48 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: N.34, C.37, D.39, C.62, C.123 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.37, A:D.39, A:D.39, A:C.62, A:C.123 ZN.16: 4 residues within 4Å: Chain B: C.37, D.39, C.62, C.123 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.37, B:D.39, B:D.39, B:C.62, B:C.123

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

NI.6: 2 residues within 4Å: Chain A: K.28, E.30 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.30, H2O.3, H2O.3 NI.7: 5 residues within 4Å: Chain A: G.1, S.2, H.3, M.4 Chain B: E.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.3 NI.8: 3 residues within 4Å: Chain A: H.20, E.58 Chain B: H.60 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.20, B:H.60, H2O.1, H2O.2, H2O.7 NI.9: 3 residues within 4Å: Chain A: H.60 Chain B: H.20, E.58 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.60, B:H.20, H2O.5, H2O.6, H2O.6 NI.17: 2 residues within 4Å: Chain B: K.28, E.30 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.30, H2O.6, H2O.10 NI.18: 5 residues within 4Å: Chain A: E.8 Chain B: G.1, S.2, H.3, M.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, H.S. et al., The sulfur formation system mediating extracellular cysteine-cystine recycling in Fervidobacterium islandicum AW-1 is associated with keratin degradation. Microb Biotechnol (2020)

Release Date

2019-10-09

Peptides

Iron-sulfur cluster assembly scaffold protein NifU: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Iron-sulfur cluster assembly scaffold protein NifU

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