SMTL ID : 5xem.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x 85F: (2R)-2-azanyl-3-[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic acid(Non-covalent)

85F.1: 17 residues within 4Å: Chain A: K.46, T.73, S.74, G.75, N.76, T.77, M.124, Q.146, F.147, G.180, T.181, G.224, M.225, G.226, M.227, S.228 Ligands: PLP.2 12 PLIP interactions: 12 interactions with chain A 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, A:G.226, A:S.228 Water bridges: A:G.226 Salt bridges: A:K.46 85F.15: 19 residues within 4Å: Chain B: K.46, T.73, S.74, G.75, N.76, T.77, M.124, Q.146, F.147, G.180, T.181, G.224, M.225, G.226, M.227, S.228 Ligands: PLP.14, PLP.16, ACT.17 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.73, B:S.74, B:S.74, B:G.75, B:N.76, B:T.77, B:Q.146, B:G.224, B:G.226, B:S.228 Water bridges: B:N.76, B:N.76, B:G.224, B:G.226, B:I.229 Salt bridges: B:K.46

3 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)(Covalent)

PLP.2: 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, M.225, S.270, T.297, D.298, Y.303 Ligands: 85F.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.297 Hydrogen bonds: A:N.76, A:G.178, A:G.180, A:T.181, A:G.182, A:G.183, A:S.184, A:S.184, A:S.270 Water bridges: A:N.76, A:N.152, A:F.185 Salt bridges: A:K.46 PLP.14: 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: 85F.15, PLP.16, ACT.17 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.46, B:T.297 Hydrogen bonds: B:N.76, B:G.178, B:G.180, B:T.181, B:G.182, B:G.183, B:S.184, B:S.270, B:T.297 Water bridges: B:R.104, B:S.184, B:S.184, B:F.185 Salt bridges: B:K.46 PLP.16: 19 residues within 4Å: Chain B: K.46, N.76, G.178, T.179, G.180, T.181, G.182, G.183, S.184, Q.223, G.224, M.225, S.270, T.297, D.298, Y.303 Ligands: PLP.14, 85F.15, ACT.17 14 PLIP interactions: 14 interactions with chain B 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.184, B:S.270, B:T.297 Water bridges: B:R.104, B:F.185 Salt bridges: B:K.46

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

ACT.3: 9 residues within 4Å: Chain A: C.85, Y.90, K.91, L.92, Y.111, G.112, T.113 Ligands: CA.5, CA.13 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.4: 3 residues within 4Å: Chain A: K.135, V.143, N.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.145 Salt bridges: A:K.135 ACT.17: 10 residues within 4Å: Chain B: K.46, T.73, S.74, G.75, N.76, T.77, Q.146 Ligands: PLP.14, 85F.15, PLP.16 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.73, B:S.74, B:G.75, B:N.76, B:T.77, B:Q.146 Water bridges: B:N.76 Salt bridges: B:K.46

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

CA.5: 2 residues within 4Å: Chain A: G.112 Ligands: ACT.3 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:G.112, H2O.2, H2O.7, H2O.7, ACT.3 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 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.250, A:D.250, H2O.1, H2O.3 CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 3 residues within 4Å: Chain A: L.304, S.305, N.306 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.304 CA.13: 1 residues within 4Å: Ligands: ACT.3 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.2, H2O.7, H2O.7, H2O.9, ACT.3 CA.18: 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.19: 1 residues within 4Å: Chain B: E.194 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.194, H2O.15, H2O.16 CA.20: 1 residues within 4Å: Chain B: D.242 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.242 CA.21: 1 residues within 4Å: Chain B: G.61 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.61, H2O.16 CA.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PEG.11: 3 residues within 4Å: Chain A: K.154, Y.157, K.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.157, A:K.190 PEG.23: 5 residues within 4Å: Chain B: V.150, P.153, K.154, Y.157, K.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.190

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.12: 6 residues within 4Å: Chain A: F.28, D.251, E.254, M.255, K.276, D.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.276

1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.24: 7 residues within 4Å: Chain B: S.121, L.122, G.123, 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-lanthionine-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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