SMTL ID : 6veb.1

Precorrin-2-bound S128A S. typhimurium siroheme synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 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, A:A.437 Water bridges: A:F.380, A:A.437, A:I.439 SAH.8: 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

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 14 residues within 4Å: Chain A: V.18, G.19, G.20, G.21, D.22, V.23, N.41, A.42, L.43, T.44, F.65, T.80, D.81, V.85 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.19, A:G.20, A:D.22, A:V.23, A:L.43, A:T.44, A:T.44, A:F.65, A:D.81, A:D.81 Water bridges: A:G.20, A:G.21, A:G.21, A:T.44

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

CL.3: 5 residues within 4Å: Chain A: T.345, H.346, D.348, Y.349, A.350 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: T.345, H.346 Chain B: F.307, R.309 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: K.142 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: A.128, G.130, S.132, P.133 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: F.307, G.308, R.309 Chain B: T.345 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: K.375, R.443 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: M.382, G.383, L.384 Ligand excluded by PLIP

1 x PQ2: 3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13,20,24-hexahydroporphyrin-2,7,1 2,18-tetrayl]tetrapropanoic acid(Covalent)

PQ2.9: 29 residues within 4Å: Chain A: R.162, K.166, M.172, R.175, R.176, W.179, Q.240, R.260, R.261, D.262 Chain B: K.27, L.30, N.101, V.103, D.104, P.106, I.112, M.113, P.114, S.115, A.128, G.129, G.130, T.131, S.132, P.133, V.134, R.137, R.140 24 PLIP interactions: 12 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:R.261, B:P.106, B:P.133, B:P.133 Hydrogen bonds: A:R.162, A:R.176, A:R.261, A:D.262, A:D.262, B:N.101, B:M.113, B:S.115, B:A.128, B:S.132 Salt bridges: A:R.162, A:K.166, A:K.166, A:R.175, A:R.260, B:K.27, B:R.137, B:R.140 pi-Cation interactions: A:R.260 Water bridges: B:K.27

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

2020-03-04

Peptides

Siroheme synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Siroheme synthase

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