SMTL ID : 6fjx.1

Structure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme with an evolutionarily-distinct C-terminal arm (Native protein)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 5 residues within 4Å: Chain A: R.272, D.416, G.417, I.418, E.419 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.272, A:R.272, A:I.418, A:E.419 PGE.10: 5 residues within 4Å: Chain C: R.272, D.416, G.417, I.418, E.419 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.272, C:R.272, C:I.418, C:E.419

4 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.2: 14 residues within 4Å: Chain A: E.124, R.127, Y.129, Q.131, R.146, I.486, W.495 Chain B: R.146, I.486 Chain D: E.124, R.127, Y.129, I.486 Ligands: BOG.14 8 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:W.495, B:I.486 Hydrogen bonds: A:E.124, D:R.127 Water bridges: A:L.128, A:Y.129, D:Y.129, D:R.146 BOG.5: 12 residues within 4Å: Chain B: E.124, R.127, I.486 Chain C: E.124, R.127, Y.129, Q.131, R.146, I.486, W.495 Chain D: I.486 Ligands: BOG.11 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.495 Hydrogen bonds: C:E.124, C:R.127, B:R.127 Water bridges: C:L.128 BOG.11: 14 residues within 4Å: Chain B: E.124, R.127, Y.129, I.486 Chain C: E.124, R.127, Y.129, Q.131, R.146, I.486, W.495 Chain D: R.146, I.486 Ligands: BOG.5 8 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:W.495, D:I.486 Hydrogen bonds: C:E.124, B:R.127 Water bridges: C:L.128, C:Y.129, B:Y.129, B:R.146 BOG.14: 12 residues within 4Å: Chain A: E.124, R.127, Y.129, Q.131, R.146, I.486, W.495 Chain B: I.486 Chain D: E.124, R.127, I.486 Ligands: BOG.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.495 Hydrogen bonds: A:E.124, A:R.127, D:R.127 Water bridges: A:L.128

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

SO4.3: 7 residues within 4Å: Chain A: F.160, R.294, T.296, V.463, G.464, A.465, F.471 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.296, A:G.464, A:A.465 Salt bridges: A:R.294 SO4.4: 4 residues within 4Å: Chain A: R.452, K.475 Chain B: G.230, Q.233 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:K.475, A:A.476 Salt bridges: A:R.452 Hydrogen bonds: B:Q.233 SO4.6: 7 residues within 4Å: Chain B: F.160, R.294, T.296, V.463, G.464, A.465, F.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.296, B:G.464, B:A.465 Salt bridges: B:R.294 SO4.7: 7 residues within 4Å: Chain B: K.182, S.184, E.185, G.213, G.214, G.215, R.342 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.185, B:G.213 Water bridges: B:K.182, B:K.182, B:N.340, B:R.342 Salt bridges: B:K.182, B:R.342 SO4.8: 3 residues within 4Å: Chain B: R.37, R.367, L.385 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.37, B:R.37 Salt bridges: B:R.37, B:R.367 SO4.9: 3 residues within 4Å: Chain A: Q.233 Chain B: R.452, K.475 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:K.475, B:K.475, B:A.476, A:L.255 Salt bridges: B:R.452 Hydrogen bonds: A:Q.233 SO4.12: 7 residues within 4Å: Chain C: F.160, R.294, T.296, V.463, G.464, A.465, F.471 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.296, C:T.296, C:G.464, C:A.465 Salt bridges: C:R.294 SO4.13: 4 residues within 4Å: Chain C: R.452, K.475 Chain D: G.230, Q.233 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Water bridges: C:K.475, C:A.476 Salt bridges: C:R.452 Hydrogen bonds: D:Q.233 SO4.15: 7 residues within 4Å: Chain D: F.160, R.294, T.296, V.463, G.464, A.465, F.471 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.296, D:T.296, D:G.464, D:A.465 Salt bridges: D:R.294 SO4.16: 7 residues within 4Å: Chain D: K.182, S.184, E.185, G.213, G.214, G.215, R.342 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.185, D:G.213 Water bridges: D:K.182, D:K.182, D:N.340, D:R.342 Salt bridges: D:K.182, D:R.342 SO4.17: 3 residues within 4Å: Chain D: R.37, R.367, L.385 4 PLIP interactions: 4 interactions with chain D Water bridges: D:R.37, D:R.37 Salt bridges: D:R.37, D:R.367 SO4.18: 3 residues within 4Å: Chain C: Q.233 Chain D: R.452, K.475 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Water bridges: D:K.475, D:K.475, D:A.476, C:L.255 Salt bridges: D:R.452 Hydrogen bonds: C:Q.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayes, K. et al., The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension. Sci Rep (2018)

Release Date

2018-09-26

Peptides

Aldehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Aldehyde dehydrogenase