SMTL ID : 4tkr.1

Native-SAD phasing for ThiT from Listeria monocytogenes serovar.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 17 residues within 4Å: Chain A: S.51, S.59, S.60, S.62, S.64, W.89, H.93, E.110, Y.111, F.115, R.155, H.159, G.163, W.167, F.180, S.181, N.185 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.180 Hydrogen bonds: A:S.62, A:S.62, A:H.159, A:N.185 Salt bridges: A:H.93, A:R.155 pi-Stacking: A:H.159, A:W.167 TPP.8: 16 residues within 4Å: Chain B: S.51, S.59, S.60, S.62, S.64, W.89, H.93, E.110, Y.111, R.155, H.159, G.163, W.167, F.180, S.181, N.185 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.167, B:W.167, B:F.180 Hydrogen bonds: B:S.62, B:R.155, B:H.159, B:N.185 Salt bridges: B:H.93, B:R.155 pi-Stacking: B:H.159, B:W.167

15 x BGL: 2-O-octyl-beta-D-glucopyranose(Non-covalent)

BGL.2: 6 residues within 4Å: Chain A: F.79, G.122, R.129 Chain B: A.154, F.157 Ligands: BGL.11 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.79, B:F.157 Hydrogen bonds: A:F.79, A:G.122, A:R.129 BGL.3: 8 residues within 4Å: Chain A: I.57, G.58, S.59, S.60, F.61, Y.170, F.172, M.184 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.57, A:F.61 Hydrogen bonds: A:S.59, A:S.60, A:F.61 BGL.4: 4 residues within 4Å: Chain A: F.172, Q.173, W.175, A.187 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.175, A:A.187 Hydrogen bonds: A:Q.173 BGL.5: 6 residues within 4Å: Chain A: I.141, E.142, W.145, S.201 Ligands: BGL.6, BGL.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.141 BGL.6: 4 residues within 4Å: Chain A: W.145, I.149, L.194 Ligands: BGL.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.145, A:W.145, A:I.149, A:L.194 BGL.7: 4 residues within 4Å: Chain A: F.124, K.139, W.143 Ligands: BGL.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.124 Hydrogen bonds: A:K.139, A:K.139 BGL.9: 4 residues within 4Å: Chain B: F.172, Q.173, W.175 Ligands: BGL.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.172, B:W.175 Hydrogen bonds: B:Q.173 BGL.10: 4 residues within 4Å: Chain B: P.54, L.55, D.56, I.57 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.57, B:I.57 Hydrogen bonds: B:P.54, B:D.56 BGL.11: 7 residues within 4Å: Chain B: Y.156, F.157, Y.160, I.182, N.185 Ligands: BGL.2, BGL.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.156, B:Y.160, B:Y.160 BGL.12: 8 residues within 4Å: Chain B: I.57, G.58, S.59, S.60, F.61, Y.170, F.172 Ligands: BGL.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.57, B:I.57, B:F.61, B:F.61 Hydrogen bonds: B:S.59, B:S.60, B:F.61 BGL.13: 4 residues within 4Å: Chain B: E.142, W.145 Ligands: BGL.15, BGL.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.142 BGL.14: 2 residues within 4Å: Chain B: L.194 Ligands: BGL.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.194 BGL.15: 4 residues within 4Å: Chain B: F.124, E.142, W.143 Ligands: BGL.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.124 BGL.16: 3 residues within 4Å: Chain B: I.182, C.189 Ligands: BGL.11 No protein-ligand interaction detected (PLIP) BGL.17: 5 residues within 4Å: Chain B: W.145, I.149, L.194 Ligands: BGL.13, BGL.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.145, B:W.145, B:I.149, B:L.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Q. et al., Multi-crystal native SAD analysis at 6 keV. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-06-18

Peptides

Thiamine transporter thia: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thiamine transporter thia