SMTL ID : 5xen.1

Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-serine-PLP Schiff base

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: K.46, N.76, G.178, T.179, G.180, T.181, G.182, G.183, S.184, G.224, S.270, T.297, D.298, Y.303 Ligands: SER.2, PLP.3 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:K.46, A:T.297, A:D.298 Hydrogen bonds: A:N.76, A:G.180, A:T.181, A:G.182, A:G.183, A:S.184, A:S.270, A:S.270, S.2 Water bridges: A:K.46, A:N.76, A:N.152, A:N.152, A:T.181, A:S.184, A:S.184, A:F.185 Salt bridges: A:K.46 PLP.3: 17 residues within 4Å: Chain A: K.46, N.76, G.178, T.179, G.180, T.181, G.182, G.183, S.184, Q.223, G.224, S.270, T.297, D.298, Y.303 Ligands: PLP.1, SER.2 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.297 Hydrogen bonds: A:N.76, A:G.180, A:T.181, A:G.182, A:G.183, A:S.184, A:S.184, A:S.270, S.2 Water bridges: A:K.46, A:R.104, A:N.152, A:T.181, A:F.185 Salt bridges: A:K.46 PLP.11: 17 residues within 4Å: Chain B: K.46, N.76, T.179, G.180, T.181, G.182, G.183, S.184, Q.223, G.224, S.270, T.297, D.298, Y.303 Ligands: SER.12, PLP.13, ACT.14 18 PLIP interactions: 17 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:K.46, B:T.297 Hydrogen bonds: B:N.76, B:G.180, B:T.181, B:G.182, B:G.183, B:S.184, B:S.184, B:S.270, B:T.297, S.12 Water bridges: B:K.46, B:N.76, B:S.184, B:S.184, B:F.185 Salt bridges: B:K.46 PLP.13: 19 residues within 4Å: Chain B: K.46, N.76, R.104, G.178, T.179, G.180, T.181, G.182, G.183, S.184, Q.223, G.224, S.270, T.297, D.298, Y.303 Ligands: PLP.11, SER.12, ACT.14 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.297 Hydrogen bonds: B:N.76, B:G.180, B:T.181, B:G.182, B:G.183, B:S.184, B:S.184, B:S.270, B:T.297, S.12 Water bridges: B:K.46, B:K.46, B:S.184, B:S.184, B:F.185 Salt bridges: B:K.46

2 x SER: SERINE(Non-covalent)

SER.2: 10 residues within 4Å: Chain A: K.46, T.73, S.74, G.75, N.76, T.77, Q.146, G.224 Ligands: PLP.1, PLP.3 15 PLIP interactions: 13 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.74, A:S.74, A:G.75, A:N.76, A:T.77, A:T.77, A:Q.146, A:G.224, S.2, S.2 Water bridges: A:K.46, A:K.46, A:N.76, A:N.76 Salt bridges: A:K.46 SER.12: 12 residues within 4Å: Chain B: K.46, T.73, S.74, G.75, N.76, T.77, Q.146, T.181, G.224 Ligands: PLP.11, PLP.13, ACT.14 13 PLIP interactions: 11 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:T.73, B:S.74, B:G.75, B:N.76, B:T.77, B:Q.146, B:G.224, S.12, S.12 Water bridges: B:N.76, B:N.76, B:T.77 Salt bridges: B:K.46

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 9 residues within 4Å: Chain A: C.85, Y.90, K.91, L.92, Y.111, G.112, T.113 Ligands: CA.5, CA.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.92 Hydrogen bonds: A:L.92, A:L.92 Water bridges: A:E.114 ACT.14: 9 residues within 4Å: Chain B: K.46, T.73, S.74, N.76, T.77, Q.146 Ligands: PLP.11, SER.12, PLP.13 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:T.73, B:S.74, B:G.75, B:N.76, B:T.77, B:Q.146, S.12 Water bridges: B:N.76, B:T.77 Salt bridges: B:K.46

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.5: 2 residues within 4Å: Chain A: G.112 Ligands: ACT.4 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:G.112, H2O.4, H2O.6, H2O.7, ACT.4 CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain A: E.60 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.60, H2O.3, H2O.5, H2O.7 CA.8: 1 residues within 4Å: Chain A: D.250 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.250, A:D.250, H2O.1 CA.10: 1 residues within 4Å: Ligands: ACT.4 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.2, H2O.7, H2O.7, H2O.9, ACT.4 CA.15: 2 residues within 4Å: Chain B: E.248, D.250 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.248, B:D.250, B:D.250, H2O.9, H2O.15 CA.16: 1 residues within 4Å: Chain B: E.194 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.194, H2O.16 CA.17: 2 residues within 4Å: Chain B: K.193, D.242 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.242, H2O.16

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

PEG.9: 2 residues within 4Å: Chain A: Y.157, K.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.157, A:K.190 PEG.18: 5 residues within 4Å: Chain B: V.150, P.153, K.154, Y.157, K.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.154, B:K.190 PEG.19: 6 residues within 4Å: Chain B: S.121, L.122, K.125, I.217, S.228, G.230 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kezuka, Y. et al., Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-serine-PLP Schiff base. To Be Published

Release Date

2018-04-11

Peptides

Cysteine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cysteine synthase

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