SMTL ID : 6jbd.1

Phosphotransferase-ATP complex related to CoA biosynthesis pathway

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.4, F.6, S.36, Y.289, K.294 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.4, A:R.4, A:S.36, A:K.294, A:K.294 Water bridges: A:N.40 GOL.2: 8 residues within 4Å: Chain A: T.12, F.15, G.140, L.141, G.142, D.143, R.155 Ligands: ATP.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.141, A:G.142, A:R.155, A:R.155 GOL.3: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.4, B:R.4, B:S.36, B:K.294, B:K.294 Water bridges: B:N.40 GOL.14: 8 residues within 4Å: Chain B: T.12, F.15, G.140, L.141, G.142, D.143, R.155 Ligands: ATP.18 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.12, B:L.141, B:G.142, B:R.155, 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.4: 3 residues within 4Å: Chain A: E.291, R.292, K.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.292 Water bridges: A:T.290 EDO.16: 3 residues within 4Å: Chain B: E.291, R.292, K.294 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.291, B:R.292 Water bridges: B:T.290

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 7 residues within 4Å: Chain A: A.149, N.168, L.169, F.170, F.171, T.290 Ligands: NA.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.149, A:F.171, A:F.171 PGE.17: 7 residues within 4Å: Chain B: A.149, N.168, L.169, F.170, F.171, T.290 Ligands: NA.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.149, B:F.171, B:F.171

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.6: 17 residues within 4Å: Chain A: G.98, Y.99, G.100, F.101, G.102, N.103, S.104, A.105, E.134, G.139, D.143, R.183, L.184, S.185, L.256 Ligands: GOL.2, MG.7 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.98, A:G.98, A:G.100, 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, A:L.184, A:S.185 Water bridges: A:Y.99, A:Y.99 ATP.18: 17 residues within 4Å: Chain B: G.98, Y.99, G.100, F.101, G.102, N.103, S.104, A.105, E.134, G.139, D.143, R.183, L.184, S.185, L.256 Ligands: GOL.14, MG.19 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.98, B:G.98, B:G.100, 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, B:L.184, B:S.185 Water bridges: B:Y.99, B:Y.99

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.7: 1 residues within 4Å: Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Ligands: ATP.18 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.8: 3 residues within 4Å: Chain A: E.21 Chain B: E.21 Ligands: CA.20 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.21, B:E.21, A:E.21, A:E.21 CA.9: 1 residues within 4Å: Chain A: D.266 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.266, A:D.266 CA.10: 2 residues within 4Å: Chain A: N.40, D.94 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.94, H2O.1, H2O.1, H2O.1, H2O.2 CA.20: 3 residues within 4Å: Chain A: E.21 Chain B: E.21 Ligands: CA.8 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.21: 1 residues within 4Å: Chain B: D.266 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.266, B:D.266 CA.22: 2 residues within 4Å: Chain B: N.40, D.94 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.94, H2O.3, H2O.3, H2O.4, H2O.4

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

NA.11: 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:G.102 Water bridges: A:T.39 NA.12: 6 residues within 4Å: Chain A: G.151, I.152, N.168, L.169, F.171 Ligands: PGE.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.152, A:N.168, A:L.169 NA.23: 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.24: 6 residues within 4Å: Chain B: G.151, I.152, N.168, L.169, F.171 Ligands: PGE.17 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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