SMTL ID : 6a6e.2 (1 other biounit)

Crystal structure of thermostable Cysteine desulfurase (FiSufS) from thermophilic Fervidobacterium Islandicum AW-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: T.103, T.104, H.133, A.135, T.183, N.187, D.210, A.212, Q.213, S.233, H.235, K.236 Chain B: G.286, T.287 Ligands: CIT.6 16 PLIP interactions: 2 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:T.287, B:T.287, A:T.104, A:T.104, A:T.104, A:Q.213, A:S.233, A:K.236 Hydrophobic interactions: A:H.133, A:A.212, A:K.236 Water bridges: A:H.133, A:N.187 Salt bridges: A:H.235, A:K.236 pi-Stacking: A:H.133 PLP.11: 15 residues within 4Å: Chain A: G.286, T.287 Chain B: T.103, T.104, H.133, A.135, Q.185, N.187, D.210, A.212, Q.213, S.233, H.235, K.236 Ligands: CIT.15 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.133, B:A.212, B:K.236 Hydrogen bonds: B:T.103, B:T.104, B:T.104, B:T.104, B:Q.213, B:S.233, B:S.233, B:K.236, A:T.287, A:T.287 Water bridges: B:H.133, B:N.187, A:N.63 Salt bridges: B:H.235, B:K.236 pi-Stacking: B:H.133

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: N.63, I.64, H.65, R.66, G.263, E.264, G.286, T.287 Chain B: C.376 Ligands: CIT.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.63, A:I.64, A:R.66, A:E.264 Water bridges: A:T.287 GOL.3: 3 residues within 4Å: Chain A: F.146, Y.147 Chain B: Y.147 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.147 GOL.4: 7 residues within 4Å: Chain A: R.199, K.203, A.205, T.206, D.228, K.249, L.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.199, A:R.199, A:T.206 GOL.12: 3 residues within 4Å: Chain B: R.142, F.146 Ligands: PEG.7 No protein-ligand interaction detected (PLIP) GOL.13: 9 residues within 4Å: Chain A: C.376 Chain B: N.63, I.64, H.65, G.263, E.264, G.286, T.287 Ligands: CIT.6 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.63, B:N.63, B:E.264 Water bridges: B:T.287, B:Q.288, A:H.133

6 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 6 residues within 4Å: Chain A: H.354, H.356, S.372, G.373, S.395 Chain B: R.66 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.356, A:S.395, B:R.66 Water bridges: A:H.356, A:H.356, A:H.374, B:R.66 Salt bridges: A:H.354, A:H.354, A:H.356, A:H.356 CIT.6: 12 residues within 4Å: Chain A: A.41, H.133, K.236, R.371, H.375, C.376, R.398 Chain B: N.63, I.64, H.65 Ligands: PLP.1, GOL.13 14 PLIP interactions: 2 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:N.63, A:A.40 Water bridges: B:T.287, A:R.371, A:H.375, A:R.398, A:R.398 Hydrophobic interactions: A:A.41, A:R.371 Salt bridges: A:H.133, A:K.236, A:R.371, A:H.375, A:R.398 CIT.9: 7 residues within 4Å: Chain A: H.65, R.66, T.76, E.80, E.264, N.277, Y.281 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.65 Hydrogen bonds: A:R.66, A:N.277, A:N.277, A:Y.281 Water bridges: A:A.67 Salt bridges: A:H.65, A:H.65 CIT.14: 7 residues within 4Å: Chain B: H.65, R.66, T.76, E.80, E.264, N.277, Y.281 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.66, B:N.277, B:Y.281 Water bridges: B:R.66, B:A.67 Salt bridges: B:H.65, B:H.65, B:H.65, B:R.66, B:R.66 CIT.15: 13 residues within 4Å: Chain A: N.63, I.64, H.65, R.66 Chain B: A.41, H.133, K.236, R.371, H.375, C.376, R.398 Ligands: GOL.2, PLP.11 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:A.40, A:R.66, A:R.66 Water bridges: B:H.375, B:H.375, B:H.375, B:R.398 Salt bridges: B:H.133, B:K.236, B:R.371, B:R.371, B:H.375, B:R.398, A:R.66 CIT.16: 7 residues within 4Å: Chain B: H.354, P.355, H.356, S.372, G.373, P.393, S.395 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.356, B:H.356, B:S.395, B:S.395 Salt bridges: B:H.354, B:H.356, B:H.356

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

PEG.7: 4 residues within 4Å: Chain A: S.117, Q.255 Ligands: PEG.8, GOL.12 No protein-ligand interaction detected (PLIP) PEG.8: 5 residues within 4Å: Chain A: S.117, G.118, I.119, Q.255 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.255 PEG.10: 3 residues within 4Å: Chain A: K.418, Y.419, R.422 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.422

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

Cysteine desulfurase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Cysteine desulfurase

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