SMTL ID : 6jbc.1

Phosphotransferase related to CoA biosynthesis pathway

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 7 residues within 4Å: Chain A: A.149, N.168, L.169, F.170, F.171, T.290 Ligands: NA.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.171 PG4.12: 7 residues within 4Å: Chain B: A.149, N.168, L.169, F.170, F.171, T.290 Ligands: NA.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.171

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.4, F.6, S.36, Y.289, K.294 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.4, A:R.4, A:S.36, A:K.294, A:K.294 GOL.3: 7 residues within 4Å: Chain A: T.12, G.140, L.141, G.142, D.143, R.155, L.256 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.12, A:L.141, A:G.142, A:D.143, A:R.155 GOL.4: 1 residues within 4Å: Chain A: Y.117 No protein-ligand interaction detected (PLIP) GOL.13: 5 residues within 4Å: Chain B: R.4, F.6, S.36, Y.289, K.294 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.4, B:R.4, B:S.36, B:K.294, B:K.294 GOL.14: 7 residues within 4Å: Chain B: T.12, G.140, L.141, G.142, D.143, R.155, L.256 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.12, B:T.12, B:L.141, B:G.142, B:D.143, B:R.155 GOL.15: 1 residues within 4Å: Chain B: Y.117 No protein-ligand interaction detected (PLIP)

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

EDO.5: 3 residues within 4Å: Chain A: E.291, R.292, K.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.292 EDO.16: 3 residues within 4Å: Chain B: E.291, R.292, K.294 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.292

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.6: 11 residues within 4Å: Chain A: N.97, G.98, G.100, F.101, G.102, N.103, S.104, A.105, E.134, G.139, D.143 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.98, A:Y.99, A:G.100, A:F.101, A:G.102, A:N.103, A:S.104, A:S.104, A:A.105, A:G.139, A:G.139 PPV.17: 11 residues within 4Å: Chain B: N.97, G.98, G.100, F.101, G.102, N.103, S.104, A.105, E.134, G.139, D.143 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.98, B:Y.99, B:G.100, B:F.101, B:G.102, B:N.103, B:S.104, B:S.104, B:A.105, B:G.139, B:G.139, B:D.143

6 x CA: CALCIUM ION(Non-covalent)

CA.7: 3 residues within 4Å: Chain A: E.21 Chain B: E.21 Ligands: CA.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.21, A:E.21, B:E.21, B:E.21 CA.8: 1 residues within 4Å: Chain A: D.266 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.266, A:D.266, H2O.1 CA.9: 2 residues within 4Å: Chain A: N.40, D.94 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.94, H2O.1, H2O.1 CA.18: 3 residues within 4Å: Chain A: E.21 Chain B: E.21 Ligands: CA.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.21, A:E.21, B:E.21, B:E.21 CA.19: 1 residues within 4Å: Chain B: D.266 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.266, B:D.266, H2O.2 CA.20: 2 residues within 4Å: Chain B: N.40, D.94 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.94, H2O.2, H2O.2

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

NA.10: 5 residues within 4Å: Chain A: A.9, T.39, F.101, G.102, N.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.39 Water bridges: A:T.39 NA.11: 4 residues within 4Å: Chain A: I.152, N.168, L.169 Ligands: PG4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.152, A:I.152, A:L.169 NA.21: 5 residues within 4Å: Chain B: A.9, T.39, F.101, G.102, N.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.39, B:G.102 Water bridges: B:T.39 NA.22: 4 residues within 4Å: Chain B: I.152, N.168, L.169 Ligands: PG4.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.152, B:I.152, B:L.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kita, A. et al., Crystal structure of pantoate kinase from Thermococcus kodakarensis. Proteins (2020)

Release Date

2020-01-29

Peptides

Pantoate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantoate kinase

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