SMTL ID : 6bwl.1

X-ray structure of Pal from Bacillus thuringiensis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 29 residues within 4Å: Chain A: G.7, A.9, G.10, F.11, I.12, D.31, N.32, L.33, A.34, N.35, S.36, G.56, D.57, I.58, K.59, L.79, A.80, A.81, I.83, N.98, M.120, S.121, Y.147, K.151, P.174, F.175, N.176, T.177 Ligands: CL.8 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:I.12 Hydrogen bonds: A:F.11, A:I.12, A:N.32, A:N.32, A:L.33, A:A.34, A:N.35, A:N.35, A:S.36, A:S.36, A:I.58, A:K.59, A:L.79, A:A.81, A:N.98, A:Y.147, A:K.151, A:T.177, A:T.177 Water bridges: A:G.10, A:G.13, A:N.98, A:N.98, A:N.176, A:Q.182, A:Q.182, A:Q.182, A:Q.182 NAD.10: 29 residues within 4Å: Chain B: G.7, A.9, G.10, F.11, I.12, D.31, N.32, L.33, A.34, N.35, S.36, G.56, D.57, I.58, K.59, L.79, A.80, A.81, I.83, N.98, M.120, S.121, Y.147, K.151, P.174, F.175, N.176, T.177 Ligands: CL.17 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.12 Hydrogen bonds: B:F.11, B:I.12, B:N.32, B:N.32, B:L.33, B:A.34, B:N.35, B:N.35, B:S.36, B:S.36, B:I.58, B:K.59, B:L.79, B:A.81, B:N.98, B:K.151, B:T.177, B:T.177 Water bridges: B:G.10, B:G.13, B:N.98, B:N.98, B:N.176, B:Q.182, B:Q.182, B:Q.182, B:Q.182

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 14 residues within 4Å: Chain A: M.124, N.176, G.189, V.190, I.193, F.194, N.205, I.206, Y.207, Q.212, R.214, I.250, H.269, E.275 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.190, A:Y.207 Hydrogen bonds: A:N.176, A:V.190, A:N.205, A:Y.207, A:Q.212, A:E.275 Water bridges: A:I.83, A:G.188, A:R.214 Salt bridges: A:R.214 UDP.11: 14 residues within 4Å: Chain B: M.124, N.176, G.189, V.190, I.193, F.194, N.205, I.206, Y.207, Q.212, R.214, I.250, H.269, E.275 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.190, B:Y.207 Hydrogen bonds: B:N.176, B:V.190, B:N.205, B:Y.207, B:Q.212, B:E.275 Water bridges: B:I.83, B:G.188, B:Y.207, B:R.214 Salt bridges: B:R.214

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

EDO.3: 4 residues within 4Å: Chain A: T.244, P.294, V.296, S.297 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.244, A:L.298 EDO.4: 7 residues within 4Å: Chain A: Y.207, G.208, D.209, G.210, Q.212, H.269, Q.277 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.207, A:D.209, A:D.209, A:G.210, A:Q.212, A:Q.212, A:Q.277 EDO.5: 8 residues within 4Å: Chain A: R.214, D.215, L.216, T.244, Q.246, D.247, I.248, L.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.215, A:D.215, A:L.216 Water bridges: A:L.298 EDO.6: 4 residues within 4Å: Chain A: M.1, K.2, K.24, E.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.26 Water bridges: A:M.1, A:K.2, A:E.26 EDO.12: 4 residues within 4Å: Chain B: T.244, P.294, V.296, S.297 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.244, B:T.244, B:L.298 EDO.13: 7 residues within 4Å: Chain B: Y.207, G.208, D.209, G.210, Q.212, H.269, Q.277 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.207, B:D.209, B:D.209, B:G.210, B:Q.212, B:Q.212, B:Q.277 EDO.14: 8 residues within 4Å: Chain B: R.214, D.215, L.216, T.244, Q.246, D.247, I.248, L.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.215, B:L.216, B:T.244 Water bridges: B:L.298 EDO.15: 4 residues within 4Å: Chain B: M.1, K.2, K.24, E.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.1, B:E.26 Water bridges: B:K.2

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

CL.7: 2 residues within 4Å: Chain A: S.249, N.251 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: T.122, Y.147 Ligands: NAD.1 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: S.249, N.251 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: T.122, Y.147 Ligands: NAD.10 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 1 residues within 4Å: Chain A: D.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.247, A:D.247, A:D.247 NA.18: 1 residues within 4Å: Chain B: D.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.247, B:D.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delvaux, N.A. et al., Molecular architectures of Pen and Pal: Key enzymes required for CMP-pseudaminic acid biosynthesis in Bacillus thuringiensis. Protein Sci. (2018)

Release Date

2018-01-17

Peptides

Pal: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pal