SMTL ID : 8a8o.1

PAPS reductase from Methanothermococcus thermolithotrophicus refined to 1.45 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-2-2-mer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 32 residues within 4Å: Chain A: G.14, G.15, G.16, A.17, A.18, V.38, E.39, K.40, S.46, G.47, C.48, L.49, V.53, N.54, A.55, N.57, T.149, I.150, A.151, T.185, T.186, G.187, W.206, Y.207, N.211, A.214, H.346, G.368, D.369, Y.378, V.379, C.382 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:W.206, A:Y.207 Hydrogen bonds: A:G.15, A:G.15, A:A.17, A:A.18, A:K.40, A:C.48, A:N.54, A:N.54, A:A.55, A:A.55, A:N.57, A:A.151, A:A.151, A:G.187, A:N.211, A:D.369, A:V.379 Water bridges: A:G.16, A:G.19, A:S.46, A:G.47, A:G.47, A:L.49, A:N.211, A:T.212, A:R.237, A:H.346, A:D.369, A:V.370 FAD.10: 32 residues within 4Å: Chain B: G.14, G.15, G.16, A.17, A.18, V.38, E.39, K.40, S.46, G.47, C.48, L.49, V.53, N.54, A.55, N.57, T.149, I.150, A.151, T.185, T.186, G.187, W.206, Y.207, N.211, A.214, H.346, G.368, D.369, Y.378, V.379, C.382 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:W.206, B:Y.207 Hydrogen bonds: B:G.15, B:G.15, B:A.17, B:A.18, B:K.40, B:C.48, B:N.54, B:A.55, B:A.55, B:N.57, B:A.151, B:A.151, B:G.187, B:N.211, B:D.369, B:V.379 Water bridges: B:G.16, B:G.19, B:K.40, B:K.40, B:S.46, B:G.47, B:G.47, B:L.49, B:N.211, B:H.346, B:D.369, B:V.370

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: I.257, A.259, P.332 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.458

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: K.307, W.321, K.322, K.325, I.326, P.328 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.321 Hydrogen bonds: A:K.307 Water bridges: A:K.322 MPD.11: 9 residues within 4Å: Chain B: N.57, A.58, Y.59, L.60, E.64, S.68, Y.69, Y.72, R.121 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.58, B:L.60, B:Y.69, B:Y.69, B:Y.72 Hydrogen bonds: B:N.57, B:Y.59, B:R.121 MPD.13: 6 residues within 4Å: Chain B: K.307, W.321, K.322, K.325, I.326, P.328 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.307, B:W.321, B:K.322 Hydrogen bonds: B:K.307, B:K.322 Water bridges: B:N.327 MPD.19: 7 residues within 4Å: Chain B: I.169, K.170, Y.483 Chain C: N.23, L.25, Y.26, M.36 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Water bridges: C:T.17, C:L.25 Hydrophobic interactions: B:I.169, B:K.170, B:Y.483 MPD.21: 7 residues within 4Å: Chain A: I.169, K.170, Y.483 Chain D: N.23, L.25, Y.26, M.36 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.169, A:K.170, A:Y.483 Water bridges: D:T.17, D:L.25

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.153, Y.154, I.155, L.156, R.221, A.222 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.156 Water bridges: A:N.153, A:N.153, A:M.218 GOL.5: 6 residues within 4Å: Chain A: L.281, C.336, G.337, I.449, Y.452, Y.453 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.337, A:I.449 GOL.6: 6 residues within 4Å: Chain A: W.352, V.353, D.354, K.358, T.359, T.360 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.354, A:K.358, A:K.358 Water bridges: A:W.352 GOL.7: 5 residues within 4Å: Chain A: Y.154, I.155, L.156, R.221 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.154, A:L.156, A:R.221 GOL.12: 5 residues within 4Å: Chain B: Y.59, N.94, A.97, K.98, E.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.94, B:E.101 Water bridges: B:K.120 GOL.14: 5 residues within 4Å: Chain B: L.281, Y.452, R.454, C.515, E.518 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.452, B:R.454, B:C.515

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 3 residues within 4Å: Chain A: H.203, E.435, R.494 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.203, A:E.435, H2O.8, H2O.8, H2O.10, H2O.11 CA.15: 2 residues within 4Å: Chain B: H.203, E.435 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.203, B:E.435, H2O.21, H2O.23, H2O.23, H2O.23

3 x NA: SODIUM ION(Non-functional Binders)

NA.9: 2 residues within 4Å: Chain A: E.472, S.475 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.475, A:S.475 Water bridges: A:S.475 NA.16: 1 residues within 4Å: Chain B: D.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.300 NA.20: 3 residues within 4Å: Chain A: E.428, K.476 Chain C: N.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.428, A:K.476

4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.17: 11 residues within 4Å: Chain C: I.3, C.20, P.21, I.35, C.41, W.42, D.43, C.44, A.45, A.46, C.47 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.20, C:C.41, C:C.44, C:C.47 SF4.18: 12 residues within 4Å: Chain C: C.10, I.11, G.12, C.13, G.14, C.16, S.33, C.51, P.52, V.53, A.55, I.56 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.10, C:C.13, C:C.16, C:C.51 SF4.22: 10 residues within 4Å: Chain D: I.3, C.20, P.21, C.41, W.42, D.43, C.44, A.45, A.46, C.47 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.20, D:C.41, D:C.44, D:C.47 SF4.23: 11 residues within 4Å: Chain D: C.10, I.11, G.12, C.13, G.14, C.16, S.33, C.51, P.52, V.53, I.56 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.10, D:C.13, D:C.16, D:C.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jespersen, M. et al., Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus. Nat Microbiol (2023)

Release Date

2023-04-26

Peptides

Alpha-subunit of the PAPS reductase from Methanothermococcus thermolithotrophicus: AB
Beta-subunit of the PAPS reductase from Methanothermococcus thermolithotrophicus: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alpha-subunit of the PAPS reductase from Methanothermococcus thermolithotrophicus

Beta-subunit of the PAPS reductase from Methanothermococcus thermolithotrophicus