SMTL ID : 8a8d.1

ATP sulfurylase from Methanothermococcus thermolithotrophicus - monoclinic form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.325, C.328, C.337, H.339 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.325, A:C.328, A:C.337, A:H.339 ZN.13: 4 residues within 4Å: Chain B: C.325, C.328, C.337, H.339 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.325, B:C.328, B:C.337, B:H.339

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.127, F.132, T.145, E.260, R.262 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.145, A:E.260 Water bridges: A:P.84, A:E.260, A:R.262, A:R.262 GOL.3: 4 residues within 4Å: Chain A: R.62, E.98, D.117, E.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.62 Water bridges: A:E.98 GOL.4: 3 residues within 4Å: Chain A: L.180, I.253, L.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.254, A:L.254 GOL.5: 1 residues within 4Å: Chain A: E.65 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.65, A:E.65 GOL.6: 4 residues within 4Å: Chain A: H.51, K.168, T.171, E.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.171

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

ACT.7: 3 residues within 4Å: Chain A: K.326, K.327, Y.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.326 ACT.8: 2 residues within 4Å: Chain A: K.94, N.95 No protein-ligand interaction detected (PLIP) ACT.9: 2 residues within 4Å: Chain A: E.345, K.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.345 Salt bridges: A:K.326, A:K.351 ACT.10: 4 residues within 4Å: Chain A: L.148, G.149, E.150 Ligands: CA.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.150 ACT.14: 2 residues within 4Å: Chain B: E.118 Ligands: CA.18 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.118, B:I.119 ACT.15: 4 residues within 4Å: Chain B: N.165, P.166, K.168, S.169 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.168, B:S.169, B:S.169 Water bridges: B:S.169, B:H.170 ACT.16: 5 residues within 4Å: Chain B: H.199, H.202, F.347, S.348, G.349 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.349 Water bridges: B:T.350 Salt bridges: B:H.199, B:H.202 ACT.17: 3 residues within 4Å: Chain B: S.377, F.378, E.379 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.379

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

EDO.11: 4 residues within 4Å: Chain A: H.199, G.201, F.322, F.347 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.322

3 x CA: CALCIUM ION(Non-covalent)

CA.12: 3 residues within 4Å: Chain A: Y.146, L.148 Ligands: ACT.10 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:Y.146, A:L.148, H2O.3, H2O.6, ACT.10 CA.18: 3 residues within 4Å: Chain B: E.98, E.118 Ligands: ACT.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.98, B:E.98, H2O.8 CA.19: 3 residues within 4Å: Chain B: Y.146, L.148, E.150 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.146, B:L.148, B:E.150, H2O.10, H2O.13

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

ATP sulfurylase from Methanothermococcus thermolithotrophicus: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP sulfurylase from Methanothermococcus thermolithotrophicus

Related Entries With Identical Sequence