SMTL ID : 6ite.1

Crystal structure of group A Streptococcal surface dehydrogenase (SDH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: N.14, G.15, F.16, G.17, R.18, I.19, N.39, D.40, L.41, E.83, R.84, A.102, T.103, G.104, F.105, F.106, T.127, A.128, C.158, N.322, Y.326 Chain B: P.197 Ligands: SO4.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.19, A:I.19, A:Y.326 Hydrogen bonds: A:F.16, A:F.16, A:R.18, A:I.19, A:N.39, A:R.84, A:N.322, A:N.322 Water bridges: A:N.14, A:N.14, A:G.17, A:G.20, A:R.84, A:G.104, A:G.189, A:G.189, A:G.189 NAD.3: 23 residues within 4Å: Chain A: P.197 Chain B: N.14, G.15, F.16, G.17, R.18, I.19, N.39, D.40, L.41, E.83, R.84, A.102, T.103, G.104, F.105, F.106, T.127, A.128, C.158, N.322, Y.326 Ligands: SO4.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.19, B:I.19, B:Y.326 Hydrogen bonds: B:F.16, B:R.18, B:I.19, B:R.84, B:T.127, B:N.322, B:N.322 Water bridges: B:N.14, B:N.14, B:G.17, B:G.20, B:R.84, B:G.104, B:T.127, B:G.189, B:G.189, B:G.189, B:G.189 NAD.6: 23 residues within 4Å: Chain C: N.14, G.15, F.16, G.17, R.18, I.19, N.39, D.40, L.41, E.83, R.84, A.102, T.103, G.104, F.105, F.106, T.127, A.128, C.158, N.322, Y.326 Chain D: P.197 Ligands: SO4.7 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.19, C:I.19, C:Y.326 Hydrogen bonds: C:F.16, C:R.18, C:I.19, C:R.84, C:T.127, C:N.322 Water bridges: C:N.14, C:N.14, C:G.17, C:G.20, C:G.104, C:T.127, C:G.189, C:G.189, D:P.197 NAD.8: 23 residues within 4Å: Chain C: P.197 Chain D: N.14, G.15, F.16, G.17, R.18, I.19, N.39, D.40, L.41, E.83, R.84, A.102, T.103, G.104, F.105, F.106, T.127, A.128, C.158, N.322, Y.326 Ligands: SO4.9 19 PLIP interactions: 1 interactions with chain C, 18 interactions with chain D Water bridges: C:P.197, D:N.14, D:N.14, D:G.17, D:G.20, D:R.84, D:G.104, D:T.127, D:G.189, D:G.189, D:G.189, D:G.189 Hydrophobic interactions: D:I.19, D:Y.326 Hydrogen bonds: D:F.16, D:R.18, D:I.19, D:R.84, D:N.322

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

SO4.2: 5 residues within 4Å: Chain A: T.188, D.190, R.205, R.241 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.190 Water bridges: A:G.189, A:G.189, A:R.205, A:R.241 Salt bridges: A:R.205, A:R.241 SO4.4: 5 residues within 4Å: Chain B: T.188, D.190, R.205, R.241 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.188, B:D.190 Water bridges: B:G.189, B:G.189, B:R.205, B:R.205 Salt bridges: B:R.205, B:R.241 SO4.5: 5 residues within 4Å: Chain B: K.178, T.255, S.311 Chain C: K.178, T.255 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Water bridges: B:Q.177, C:Q.177, C:S.311, C:S.311 Salt bridges: B:K.178, C:K.178 SO4.7: 4 residues within 4Å: Chain C: T.188, R.205, R.241 Ligands: NAD.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.188 Salt bridges: C:R.205, C:R.241 SO4.9: 5 residues within 4Å: Chain D: T.188, D.190, R.205, R.241 Ligands: NAD.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.188, D:D.190 Water bridges: D:G.189, D:G.189 Salt bridges: D:R.205, D:R.241 SO4.10: 6 residues within 4Å: Chain A: K.178, T.255, S.311 Chain D: K.178, T.255, S.311 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Water bridges: D:Q.177, D:K.178, D:S.311, A:Q.177 Salt bridges: D:K.178, A:K.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, R. et al., Structural determination of group A Streptococcal surface dehydrogenase and characterization of its interaction with urokinase-type plasminogen activator receptor. Biochem.Biophys.Res.Commun. (2019)

Release Date

2019-09-25

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
Q

C
R

D
O

Glyceraldehyde-3-phosphate dehydrogenase