SMTL ID : 5b8h.1

Crystal Structure of Type III pantothenate kinase (PanK III) from Burkholderia cenocepacia complexed with pantothenate, imidodiphosphate, and AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 2PN: IMIDODIPHOSPHORIC ACID(Non-covalent)

2PN.1: 8 residues within 4Å: Chain A: G.35, N.36, S.37, R.38, K.40, F.151, G.152, T.153 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.36, A:S.37, A:R.38, A:F.151, A:T.153 Water bridges: A:D.33, A:T.153, A:A.154, A:G.251 2PN.5: 8 residues within 4Å: Chain B: G.35, N.36, S.37, R.38, K.40, F.151, G.152, T.153 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.35, B:N.36, B:S.37, B:R.38, B:T.153 Water bridges: B:F.151, B:A.154, B:G.251

2 x PAU: PANTOTHENOIC ACID(Non-covalent)

PAU.2: 13 residues within 4Å: Chain A: N.36, V.82, Y.120, Q.125, L.126, G.127, D.129, R.130, T.156, I.171 Chain B: Q.188, L.189, T.213 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.156, A:I.171, B:L.189, B:T.213 Hydrogen bonds: A:Y.120, A:G.127, A:D.129 Water bridges: A:N.36, B:Q.188 Salt bridges: A:R.130 PAU.6: 13 residues within 4Å: Chain A: Q.188, L.189, T.213 Chain B: N.36, V.82, Y.120, Q.125, L.126, G.127, D.129, R.130, T.156, I.171 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.156, B:I.171, A:L.189, A:T.213 Hydrogen bonds: B:Y.120, B:G.127, B:D.129, A:T.213 Water bridges: B:N.36, B:D.129, B:D.129, A:Q.188 Salt bridges: B:R.130

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

EDO.3: 5 residues within 4Å: Chain A: H.58, T.59, R.60, D.86, V.87 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.59, A:R.60 Water bridges: A:H.58, A:H.58 EDO.7: 4 residues within 4Å: Chain B: I.107, R.108, R.110, Q.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.108, B:R.110, B:Q.113, B:Q.113

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 7 residues within 4Å: Chain A: T.105, T.106, I.107, R.108, R.110, Q.113, I.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.108, A:R.108, A:R.110, A:Q.113 pi-Cation interactions: A:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

SSGCID et al., Crystal Structure of Type III pantothenate kinase (PanK III) from Burkholderia cenocepacia complexed with pantothenate, imidodiphosphate, and AMP. to be published

Release Date

2015-05-13

Peptides

Type III pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Type III pantothenate kinase