SMTL ID : 8a8h.1 (1 other biounit)

APS kinase from Methanothermococcus thermolithotrophicus refined to 1.77 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Y.123, E.160, P.161, P.164, K.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.167 Water bridges: A:E.160, A:E.160 EDO.2: 5 residues within 4Å: Chain A: E.77, N.80, R.81, V.108, Y.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.80, A:R.81 EDO.3: 3 residues within 4Å: Chain A: H.85, K.88, E.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.88, A:E.115 Water bridges: A:E.115 EDO.4: 4 residues within 4Å: Chain A: R.76, I.102, S.103, P.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.76, A:N.80, A:I.102 EDO.5: 4 residues within 4Å: Chain A: K.73, R.76, Y.105, A.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.73, A:R.76 Water bridges: A:A.107 EDO.8: 4 residues within 4Å: Chain B: E.77, N.80, V.108, Y.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.80 EDO.9: 5 residues within 4Å: Chain B: Y.123, E.160, P.161, P.164, K.167 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.160, B:E.160 EDO.10: 3 residues within 4Å: Chain B: L.189, G.190, Y.191 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.190 Water bridges: B:N.118

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 7 residues within 4Å: Chain A: P.30, S.31, G.32, A.33, G.34, K.35, S.36 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.31, A:G.32, A:G.32, A:A.33, A:G.34, A:K.35, A:S.36 Water bridges: A:K.35, A:K.35, A:S.100 Salt bridges: A:K.35 PO4.11: 7 residues within 4Å: Chain B: P.30, S.31, G.32, A.33, G.34, K.35, S.36 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.32, B:A.33, B:G.34, B:K.35, B:S.36 Water bridges: B:G.32, B:T.37 Salt bridges: B:K.35

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

CL.7: 1 residues within 4Å: Chain A: K.49 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: K.49 Ligand excluded by PLIP

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

APS kinase from Methanothermococcus thermolithotrophicus: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

APS kinase from Methanothermococcus thermolithotrophicus

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