SMTL ID : 3otw.1

Structural and Functional Studies of Helicobacter pylori Wild-Type and Mutated Proteins Phosphopantetheine adenylyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: H.44, S.53, L.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.54 Water bridges: A:S.53, A:D.55, A:R.57 Salt bridges: A:H.44 SO4.3: 3 residues within 4Å: Chain B: H.44, S.53, L.54 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.54 Water bridges: B:D.55, B:R.57 Salt bridges: B:H.44 SO4.4: 2 residues within 4Å: Chain B: S.136, R.139 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.139 Salt bridges: B:R.139 SO4.6: 3 residues within 4Å: Chain C: H.44, S.53, L.54 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.54 Water bridges: C:S.53, C:D.55, C:R.57 Salt bridges: C:H.44 SO4.8: 4 residues within 4Å: Chain D: H.44, S.53, L.54, R.57 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.54, D:R.57 Salt bridges: D:H.44 SO4.10: 1 residues within 4Å: Chain E: R.139 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.139 SO4.11: 3 residues within 4Å: Chain E: H.44, S.53, L.54 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.54 Water bridges: E:R.57 Salt bridges: E:H.44

6 x COA: COENZYME A(Non-covalent)

COA.2: 24 residues within 4Å: Chain A: P.14, G.15, T.16, T.21, G.23, H.24, A.43, K.48, F.76, G.78, L.79, L.80, R.94, R.97, Y.104, A.111, N.112, I.133, S.134, S.135, S.136, R.139 Chain D: S.140, H.144 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:P.14, A:A.43 Hydrogen bonds: A:Y.13, A:T.16, A:T.16, A:T.21, A:G.23, A:L.80, A:R.97, A:R.97, A:S.134, A:S.135, A:S.136, D:S.140, D:S.140 Water bridges: A:F.17, A:A.81, A:R.94, A:N.112, A:S.136 Salt bridges: A:K.48, A:K.48, A:K.48, A:R.94, A:R.94, A:R.139 pi-Stacking: A:H.24, A:H.24 COA.5: 25 residues within 4Å: Chain B: P.14, G.15, T.16, T.21, G.23, H.24, A.43, K.48, F.76, G.78, L.79, L.80, R.94, R.97, Y.104, M.108, A.111, N.112, I.133, S.134, S.135, S.136, R.139 Chain C: S.140, H.144 26 PLIP interactions: 24 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.14, B:A.43 Hydrogen bonds: B:T.16, B:G.23, B:L.80, B:R.97, B:R.97, B:Y.104, B:Y.104, B:S.135, B:S.136, C:S.140, C:S.140 Water bridges: B:D.18, B:A.81, B:R.94, B:S.134, B:S.135 Salt bridges: B:K.48, B:K.48, B:K.48, B:R.94, B:R.94, B:R.139 pi-Stacking: B:H.24, B:H.24 COA.7: 24 residues within 4Å: Chain C: P.14, G.15, T.16, T.21, G.23, H.24, A.43, K.48, F.76, G.78, L.79, L.80, R.94, R.97, Y.104, M.108, N.112, I.133, S.134, S.135, S.136, R.139 Chain E: S.140, H.144 29 PLIP interactions: 27 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:P.14, C:A.43 Hydrogen bonds: C:Y.13, C:T.16, C:T.21, C:G.23, C:L.80, C:R.97, C:R.97, C:Y.104, C:S.134, C:S.135, C:S.136, E:S.140, E:S.140 Water bridges: C:A.81, C:R.94, C:Y.104, C:Y.104, C:N.112, C:S.136 Salt bridges: C:K.48, C:K.48, C:K.48, C:R.94, C:R.94, C:R.139 pi-Stacking: C:H.24, C:H.24 COA.9: 24 residues within 4Å: Chain D: P.14, G.15, T.16, T.21, G.23, H.24, A.43, K.48, F.76, G.78, L.79, L.80, R.94, R.97, Y.104, A.111, N.112, I.133, S.134, S.135, S.136, R.139 Chain F: S.140, H.144 29 PLIP interactions: 3 interactions with chain F, 26 interactions with chain D Hydrogen bonds: F:S.140, F:S.140, D:T.16, D:T.16, D:G.23, D:L.80, D:R.97, D:R.97, D:Y.104, D:Y.104, D:S.134, D:S.135, D:S.136 Water bridges: F:H.144, D:A.81, D:R.94, D:S.135, D:S.136, D:S.136 Hydrophobic interactions: D:P.14, D:A.43 Salt bridges: D:K.48, D:K.48, D:K.48, D:R.94, D:R.94, D:R.139 pi-Stacking: D:H.24, D:H.24 COA.12: 23 residues within 4Å: Chain B: H.144 Chain E: P.14, G.15, T.16, T.21, G.23, H.24, A.43, K.48, F.76, G.78, L.79, L.80, R.94, R.97, Y.104, A.111, N.112, I.133, S.134, S.135, S.136, R.139 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:P.14, E:A.43 Hydrogen bonds: E:T.16, E:G.23, E:L.80, E:R.97, E:R.97, E:Y.104, E:S.135, E:S.136 Water bridges: E:D.18, E:A.81, E:R.94, E:N.112, E:S.134 Salt bridges: E:K.48, E:K.48, E:K.48, E:R.94, E:R.94, E:R.139 pi-Stacking: E:H.24, E:H.24 COA.13: 25 residues within 4Å: Chain A: H.144 Chain F: P.14, G.15, T.16, F.17, T.21, G.23, H.24, A.43, K.48, F.76, G.78, L.79, L.80, R.94, R.97, Y.104, M.108, A.111, N.112, I.133, S.134, S.135, S.136, R.139 31 PLIP interactions: 31 interactions with chain F Hydrophobic interactions: F:P.14, F:A.43 Hydrogen bonds: F:T.16, F:T.16, F:F.17, F:T.21, F:G.23, F:H.24, F:H.24, F:K.48, F:K.48, F:L.80, F:R.97, F:Y.104, F:Y.104, F:S.135, F:S.135, F:S.136 Water bridges: F:Y.13, F:A.81, F:R.139, F:R.139 Salt bridges: F:K.48, F:K.48, F:R.94, F:R.94, F:R.139 pi-Cation interactions: F:H.24, F:H.24, F:R.97, F:R.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, H.S. et al., Structural and Functional Studies of Helicobacter pylori Wild-Type and Mutated Proteins Phosphopantetheine adenylyltransferase. To be Published

Release Date

2011-09-14

Peptides

Phosphopantetheine adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Phosphopantetheine adenylyltransferase