SMTL ID : 6p5x.1

Sirohydrochlorin-bound S. typhimurium siroheme synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 18 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 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 Water bridges: A:F.380, A:L.384, A:A.437, A:A.437 SAH.4: 19 residues within 4Å: Chain B: P.225, L.250, 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 10 PLIP interactions: 10 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, B:A.437 Water bridges: B:L.384

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

CL.2: 4 residues within 4Å: Chain A: F.307, G.308, R.309 Chain B: T.345 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: E.374, Q.400, M.403 Ligand excluded by PLIP

1 x SHN: 3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic acid(Non-covalent)

SHN.5: 30 residues within 4Å: Chain A: R.162, K.166, M.172, R.175, R.176, W.179, R.260, R.261, D.262 Chain B: K.27, N.101, D.104, A.105, P.106, F.111, I.112, M.113, P.114, S.115, S.127, A.128, G.129, G.130, T.131, S.132, P.133, V.134, A.136, R.137, R.140 32 PLIP interactions: 15 interactions with chain B, 17 interactions with chain A Hydrophobic interactions: B:P.133, B:A.136 Hydrogen bonds: B:A.105, B:M.113, B:A.128, B:G.129, B:G.130, B:S.132, A:R.261, A:D.262 Water bridges: B:K.27, B:N.101, B:V.134, B:R.140, A:R.162, A:R.162, A:R.162, A:R.162, A:R.261, A:D.262, A:D.262 Salt bridges: B:K.27, B:R.137, B:R.140, A:R.162, A:R.162, A:K.166, A:R.175, A:R.176, A:R.260, A:R.261 pi-Cation interactions: A:R.162

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

2020-02-26

Peptides

Siroheme synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Siroheme synthase

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