SMTL ID : 6p5z.1

Cobalt-sirohydrochlorin-bound S. typhimurium siroheme synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 19 residues within 4Å: Chain A: P.225, L.250, G.301, G.302, D.303, I.306, F.307, T.331, A.332, C.336, Y.381, M.382, V.408, N.410, G.411, P.436, A.437, L.438 Ligands: F0X.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.381 Hydrogen bonds: A:D.303, A:I.306, A:A.332, A:M.382, A:G.411, A:G.411, A:A.437 Water bridges: A:F.380, A:L.384, A:A.437 SAH.5: 18 residues within 4Å: Chain B: P.225, G.301, G.302, D.303, I.306, F.307, G.308, T.331, A.332, C.336, Y.381, M.382, V.408, N.410, G.411, P.436, A.437, L.438 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.381 Hydrogen bonds: B:D.303, B:I.306, B:A.332, B:M.382, B:G.411, B:G.411, B:A.437

2 x F0X: cobalt-sirohydrochlorin(Non-covalent)(Covalent)

F0X.2: 8 residues within 4Å: Chain A: V.23, R.26, K.27, V.103, R.137, R.140 Chain B: K.166, M.172 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:V.23, A:V.23, A:V.103 Hydrogen bonds: A:R.26 Salt bridges: A:K.27, A:R.137, A:R.140, B:K.166, B:R.176 F0X.3: 13 residues within 4Å: Chain A: K.270, Q.279, F.307, R.309, H.359, L.360, T.362, M.382, G.383, L.384, N.385, S.435 Ligands: SAH.1 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:M.382 Hydrogen bonds: A:L.384, A:N.385, A:N.385, A:S.435, A:S.435 Salt bridges: A:R.249, A:R.309, A:R.309, A:H.359 Metal complexes: A:H.359

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: F.307, G.308, R.309 Chain B: T.345 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain B: A.128, G.129, G.130, T.131, S.132, P.133 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pennington, J.M. et al., Siroheme synthase orients substrates for dehydrogenase and chelatase activities in a common active site. Nat Commun (2020)

Release Date

2021-06-16

Peptides

Siroheme synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Siroheme synthase

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