SMTL ID : 1o6b.2 (1 other biounit)

Crystal structure of phosphopantetheine adenylyltransferase with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: H.18, R.91, S.128, S.129, S.130 Ligands: ADP.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.129, A:S.130 Water bridges: A:S.129, A:S.129 Salt bridges: A:H.18, A:R.91 PO4.5: 6 residues within 4Å: Chain B: H.18, R.91, S.128, S.129, S.130 Ligands: ADP.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.129, B:S.130 Water bridges: B:S.129, B:S.129 Salt bridges: B:H.18, B:R.91 PO4.9: 6 residues within 4Å: Chain C: H.18, R.91, S.128, S.129, S.130 Ligands: ADP.12 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.129, C:S.130 Water bridges: C:S.129, C:S.129 Salt bridges: C:H.18, C:R.91 PO4.13: 6 residues within 4Å: Chain D: H.18, R.91, S.128, S.129, S.130 Ligands: ADP.16 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.129, D:S.130 Water bridges: D:S.129, D:S.129 Salt bridges: D:H.18, D:R.91 PO4.17: 6 residues within 4Å: Chain E: H.18, R.91, S.128, S.129, S.130 Ligands: ADP.20 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.129, E:S.130 Water bridges: E:S.129, E:S.129 Salt bridges: E:H.18, E:R.91 PO4.21: 6 residues within 4Å: Chain F: H.18, R.91, S.128, S.129, S.130 Ligands: ADP.24 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.129, F:S.130 Water bridges: F:S.129, F:S.129 Salt bridges: F:H.18, F:R.91

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.139 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.139, H2O.1, H2O.2 MG.6: 1 residues within 4Å: Chain B: D.139 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.139, H2O.5, H2O.7 MG.10: 1 residues within 4Å: Chain C: D.139 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.139, H2O.9, H2O.11 MG.14: 1 residues within 4Å: Chain D: D.139 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.139, H2O.14, H2O.15 MG.18: 1 residues within 4Å: Chain E: D.139 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.139, H2O.18, H2O.20 MG.22: 1 residues within 4Å: Chain F: D.139 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.139, H2O.22, H2O.24

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

CL.3: 5 residues within 4Å: Chain A: S.3, K.84 Chain E: S.3, K.84 Ligands: CL.19 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: S.3, K.84 Chain D: S.3, K.84 Ligands: CL.15 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain C: S.3, K.84 Chain F: S.3, K.84 Ligands: CL.23 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: S.3, K.84 Chain D: S.3, K.84 Ligands: CL.7 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: S.3, K.84 Chain E: S.3, K.84 Ligands: CL.3 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain C: S.3, K.84 Chain F: S.3, K.84 Ligands: CL.11 Ligand excluded by PLIP

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

ADP.4: 15 residues within 4Å: Chain A: P.8, G.9, S.10, F.11, G.17, H.18, I.21, L.87, R.88, G.89, R.91, A.120, Y.124, L.127 Ligands: PO4.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.10, A:F.11, A:L.87, A:G.89, A:Y.124 Water bridges: A:D.12, A:T.15 Salt bridges: A:H.18, A:R.88, A:R.88 ADP.8: 15 residues within 4Å: Chain B: P.8, G.9, S.10, F.11, G.17, H.18, I.21, L.87, R.88, G.89, R.91, A.120, Y.124, L.127 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.10, B:F.11, B:L.87, B:G.89, B:Y.124 Water bridges: B:D.12 Salt bridges: B:H.18, B:R.88, B:R.88 ADP.12: 15 residues within 4Å: Chain C: P.8, G.9, S.10, F.11, G.17, H.18, I.21, L.87, R.88, G.89, R.91, A.120, Y.124, L.127 Ligands: PO4.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.10, C:F.11, C:L.87, C:G.89, C:Y.124 Water bridges: C:D.12 Salt bridges: C:H.18, C:R.88, C:R.88 ADP.16: 15 residues within 4Å: Chain D: P.8, G.9, S.10, F.11, G.17, H.18, I.21, L.87, R.88, G.89, R.91, A.120, Y.124, L.127 Ligands: PO4.13 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.10, D:F.11, D:L.87, D:G.89, D:Y.124 Water bridges: D:S.10, D:D.12 Salt bridges: D:H.18, D:R.88, D:R.88 ADP.20: 15 residues within 4Å: Chain E: P.8, G.9, S.10, F.11, G.17, H.18, I.21, L.87, R.88, G.89, R.91, A.120, Y.124, L.127 Ligands: PO4.17 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.10, E:F.11, E:L.87, E:G.89, E:Y.124 Water bridges: E:D.12, E:T.15 Salt bridges: E:H.18, E:R.88, E:R.88 ADP.24: 15 residues within 4Å: Chain F: P.8, G.9, S.10, F.11, G.17, H.18, I.21, L.87, R.88, G.89, R.91, A.120, Y.124, L.127 Ligands: PO4.21 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:S.10, F:F.11, F:L.87, F:G.89, F:Y.124 Water bridges: F:D.12, F:T.15 Salt bridges: F:H.18, F:R.88, F:R.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Badger, J. et al., Structural analysis of a set of proteins resulting from a bacterial genomics project. Proteins (2005)

Release Date

2003-11-25

Peptides

Phosphopantetheine adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Phosphopantetheine adenylyltransferase

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