SMTL ID : 5e26.2 (1 other biounit)

Crystal structure of human PANK2: the catalytic core domain in complex with pantothenate and adenosine diphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: G.16, G.17, T.18, L.19, K.21, R.83, G.188, S.189, G.212, G.213, F.216, F.228, E.229, G.318, N.319, F.320, R.322 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.17, A:T.18, A:T.18, A:T.18, A:L.19, A:R.83, A:S.189, A:G.212, A:E.229, A:N.319, A:N.319, A:F.320, A:R.322 Water bridges: A:D.14, A:K.21, A:K.21, A:G.190, A:G.352 Salt bridges: A:K.21, A:K.21 pi-Stacking: A:F.228 ADP.5: 17 residues within 4Å: Chain B: G.16, G.17, T.18, L.19, K.21, R.83, G.188, S.189, G.212, G.213, F.216, F.228, E.229, G.318, N.319, F.320, R.322 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.17, B:T.18, B:L.19, B:L.19, B:S.189, B:G.212, B:E.229, B:N.319, B:N.319, B:F.320, B:R.322 Water bridges: B:D.14, B:D.14, B:K.21, B:K.21 Salt bridges: B:K.21, B:K.21 pi-Stacking: B:F.228

2 x PAU: PANTOTHENOIC ACID(Non-covalent)

PAU.2: 11 residues within 4Å: Chain A: E.135, G.190, V.191, S.192, R.204, G.207, T.208, S.209 Chain B: Y.255, V.265, A.266 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.190, A:V.191, A:R.204, B:A.266 Water bridges: A:E.135, A:E.135, A:G.190, A:S.192, B:V.265 Salt bridges: A:R.204 Hydrophobic interactions: B:Y.255, B:A.266 PAU.4: 13 residues within 4Å: Chain A: V.247, Y.255, V.265, A.266 Chain B: E.135, G.190, V.191, S.192, R.204, G.207, T.208, S.209 Ligands: UNX.9 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.247, A:Y.255 Hydrogen bonds: A:A.266, B:G.190, B:V.191, B:R.204, B:S.209 Water bridges: B:E.135, B:E.135, B:E.135, B:G.190, B:S.192 Salt bridges: B:R.204

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

UNX.3: 3 residues within 4Å: Chain A: Y.255, E.256, R.257 No protein-ligand interaction detected (PLIP) UNX.8: 6 residues within 4Å: Chain A: I.250 Chain B: I.15, G.16, T.86, G.114, F.118 No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain B: R.204, G.207 Ligands: PAU.4 No protein-ligand interaction detected (PLIP) UNX.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain B: D.147, C.157, D.175, L.176, P.179, L.346 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.175, B:L.176

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

CL.7: 6 residues within 4Å: Chain B: F.8, P.9, Y.24, P.27, L.42, R.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

LOPPNAU, P. et al., Crystal structure of human PANK2: the catalytic core domain in complex with pantothenate and adenosine diphosphate. to be published

Release Date

2015-10-21

Peptides

Pantothenate kinase 2, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Pantothenate kinase 2, mitochondrial

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