SMTL ID : 3sms.1

Human Pantothenate kinase 3 in complex with a pantothenate analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 19 residues within 4Å: Chain A: G.29, G.30, T.31, L.32, K.34, R.96, G.201, S.202, G.225, G.226, F.241, E.242, G.331, N.332, F.333, R.335 Ligands: UNX.3, UNX.10, UNX.12 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.30, A:T.31, A:L.32, A:R.96, A:S.202, A:G.225, A:E.242, A:N.332, A:N.332, A:F.333, A:R.335 Water bridges: A:K.34, A:K.34, A:G.203, A:R.335 Salt bridges: A:K.34, A:K.34 pi-Stacking: A:F.241 ADP.14: 19 residues within 4Å: Chain B: G.29, G.30, T.31, L.32, K.34, R.96, G.201, S.202, G.225, G.226, F.241, E.242, G.331, N.332, F.333, R.335 Ligands: UNX.16, UNX.23, UNX.25 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.30, B:T.31, B:L.32, B:R.96, B:S.202, B:G.225, B:E.242, B:N.332, B:N.332, B:F.333, B:R.335 Water bridges: B:T.31, B:K.34, B:K.34, B:G.203, B:R.335 Salt bridges: B:K.34, B:K.34 pi-Stacking: B:F.241

2 x RNH: (2R)-N-[3-(heptylamino)-3-oxopropyl]-2,4-dihydroxy-3,3-dimethylbutanamide(Non-covalent)

RNH.2: 18 residues within 4Å: Chain A: E.148, G.203, V.204, S.205, R.217, G.220, T.221 Chain B: V.260, Y.268, V.278, A.279, G.312, S.313, R.316, A.347, W.351 Ligands: UNX.3, UNX.10 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:V.260, B:Y.268, B:R.316, B:A.347, B:W.351, B:W.351 Hydrogen bonds: B:V.278, B:A.279, B:A.279, A:G.203, A:V.204, A:R.217, A:R.217 Water bridges: A:E.148, A:E.148, A:E.148, A:G.220 RNH.15: 18 residues within 4Å: Chain A: V.260, Y.268, V.278, A.279, G.312, S.313, R.316, A.347, W.351 Chain B: E.148, G.203, V.204, S.205, R.217, G.220, T.221 Ligands: UNX.16, UNX.23 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:G.203, B:V.204, B:R.217, B:R.217, A:V.278, A:A.279, A:A.279 Water bridges: B:E.148, B:E.148, B:G.220 Hydrophobic interactions: A:V.260, A:Y.268, A:R.316, A:A.347, A:W.351, A:W.351

22 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 6 residues within 4Å: Chain A: E.148, N.199 Ligands: ADP.1, RNH.2, UNX.10, UNX.12 Ligand excluded by PLIP UNX.4: 2 residues within 4Å: Chain A: S.70, T.71 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: T.338, L.339 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: V.305, N.309, L.343 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: N.65, V.66, A.67 Ligand excluded by PLIP UNX.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: R.261, G.275, W.276 Ligand excluded by PLIP UNX.10: 7 residues within 4Å: Chain A: G.29, G.30 Chain B: I.263 Ligands: ADP.1, RNH.2, UNX.3, UNX.12 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: A.277, V.278 Ligand excluded by PLIP UNX.12: 7 residues within 4Å: Chain A: D.27, G.29, G.125, E.148 Ligands: ADP.1, UNX.3, UNX.10 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: D.267, Y.268, E.269 Ligand excluded by PLIP UNX.16: 6 residues within 4Å: Chain B: E.148, N.199 Ligands: ADP.14, RNH.15, UNX.23, UNX.25 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain B: S.70, T.71 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain B: T.338, L.339 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain B: V.305, N.309, L.343 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain B: N.65, V.66, A.67 Ligand excluded by PLIP UNX.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.22: 3 residues within 4Å: Chain B: R.261, G.275, W.276 Ligand excluded by PLIP UNX.23: 7 residues within 4Å: Chain A: I.263 Chain B: G.29, G.30 Ligands: ADP.14, RNH.15, UNX.16, UNX.25 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain B: A.277, V.278 Ligand excluded by PLIP UNX.25: 7 residues within 4Å: Chain B: D.27, G.29, G.125, E.148 Ligands: ADP.14, UNX.16, UNX.23 Ligand excluded by PLIP UNX.26: 3 residues within 4Å: Chain B: D.267, Y.268, E.269 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mottaghi, K. et al., Human Pantothenate kinase 3 in complex with a pantothenate analog. to be published

Release Date

2011-07-13

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3