SMTL ID : 4lrt.1

Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-oligomer

Ligands

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 11 residues within 4Å: Chain A: R.21, D.22, L.92, F.143, M.145, V.173, S.175, H.204, H.206, Y.295 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.92, A:F.143 Hydrogen bonds: A:R.21, A:R.21, A:Y.295 Water bridges: A:H.206, A:S.296 Salt bridges: A:H.204, A:H.206 PYR.9: 11 residues within 4Å: Chain C: R.21, D.22, L.92, F.143, M.145, V.173, S.175, H.204, H.206, Y.295 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.92, C:F.143 Hydrogen bonds: C:R.21, C:R.21, C:Y.295 Water bridges: C:S.296 Salt bridges: C:H.204, C:H.206

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

NA.2: 4 residues within 4Å: Chain A: V.180, L.181, S.182 Chain C: Q.221 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:V.180, A:S.182, C:Q.221 Water bridges: A:D.183 NA.5: 3 residues within 4Å: Chain B: K.98, L.101, A.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.102 NA.6: 3 residues within 4Å: Chain B: I.173, N.296 Ligands: COA.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.296 Water bridges: B:T.182 NA.14: 3 residues within 4Å: Chain D: I.173, N.296 Ligands: COA.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.296

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.22, H.204, H.206 Ligands: PYR.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.22, A:H.204, A:H.206, H2O.2 MG.12: 4 residues within 4Å: Chain C: D.22, H.204, H.206 Ligands: PYR.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.22, C:H.204, C:H.206, H2O.29

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

SO4.4: 3 residues within 4Å: Chain B: R.268, D.269, I.270 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.269, B:I.270 Water bridges: B:P.267, B:R.268, B:D.269 Salt bridges: B:R.268 SO4.13: 2 residues within 4Å: Chain D: A.247, R.251 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.251, D:R.251 Salt bridges: D:R.251

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain B: A.108, P.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.108 Water bridges: B:A.108 GOL.10: 3 residues within 4Å: Chain C: I.161, D.164, A.165 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.161, C:D.164 GOL.11: 4 residues within 4Å: Chain C: A.306, P.312, A.313, H.314 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.313, C:H.314, C:H.314 Water bridges: C:R.284, C:R.284

2 x COA: COENZYME A(Non-covalent)

COA.8: 22 residues within 4Å: Chain B: V.29, G.30, P.31, G.32, N.33, I.34, V.54, G.55, V.56, S.60, A.94, T.95, S.96, A.99, T.118, P.119, C.146, G.181, T.182, N.296, L.297 Ligands: NA.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.34, B:T.118 Hydrogen bonds: B:P.31, B:N.33, B:N.33, B:I.34, B:T.182, B:T.182 Water bridges: B:G.32, B:G.35, B:E.61, B:G.62, B:A.97, B:K.98, B:N.103, B:T.182, B:T.182 COA.15: 23 residues within 4Å: Chain D: V.29, G.30, P.31, G.32, N.33, I.34, V.54, G.55, V.56, S.60, A.94, T.95, S.96, A.99, L.117, T.118, P.119, C.146, G.181, T.182, N.296, L.297 Ligands: NA.14 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.34, D:T.118 Hydrogen bonds: D:P.31, D:N.33, D:N.33, D:I.34, D:T.182 Water bridges: D:G.32, D:N.33, D:G.35, D:T.95, D:A.97, D:N.103, D:N.103, D:T.182, D:T.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fischer, B. et al., Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site. To be Published

Release Date

2013-09-04

Peptides

4-hydroxy-2-oxovalerate aldolase: AC
Acetaldehyde dehydrogenase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

4-hydroxy-2-oxovalerate aldolase

Acetaldehyde dehydrogenase

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