SMTL ID : 4lrs.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 Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: G.151, P.152, E.153, E.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.151, A:E.153, A:E.154 Water bridges: A:E.154 SO4.21: 4 residues within 4Å: Chain C: G.151, P.152, E.153, E.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.151, C:E.153, C:E.154

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 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.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.92, A:F.143 Hydrogen bonds: A:R.21, A:R.21 Water bridges: A:S.296 Salt bridges: A:H.204, A:H.206 PYR.22: 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.24 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 CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: V.180, L.181, S.182 Chain C: Q.221 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain B: L.258, T.260, E.261, P.262, A.278, V.279, F.280 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: Q.221 Chain C: V.180, L.181, S.182 Ligand excluded by PLIP CL.32: 7 residues within 4Å: Chain D: L.258, T.260, E.261, P.262, A.278, V.279, F.280 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.22, H.204, H.206 Ligands: PYR.2 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.24: 4 residues within 4Å: Chain C: D.22, H.204, H.206 Ligands: PYR.22 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.22, C:H.204, C:H.206, H2O.24

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: D.183 Chain C: R.252, L.253 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.183, C:R.252 GOL.13: 4 residues within 4Å: Chain B: A.233, D.234, T.235 Ligands: GOL.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.235, B:T.235 Water bridges: B:P.231, B:T.235, B:D.236 GOL.14: 3 residues within 4Å: Chain B: R.268, D.269, I.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.268, B:D.269, B:I.270 GOL.15: 10 residues within 4Å: Chain B: I.229, P.231, T.235, Y.264, D.265, Q.266, P.267, A.275, R.276 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.265, B:R.276 GOL.16: 3 residues within 4Å: Chain B: T.257, L.258, R.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.257 Water bridges: B:R.259, B:R.284 GOL.17: 2 residues within 4Å: Chain B: P.231, D.232 No protein-ligand interaction detected (PLIP) GOL.25: 3 residues within 4Å: Chain A: R.252, L.253 Chain C: D.183 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.183, A:R.252 GOL.33: 4 residues within 4Å: Chain D: A.233, D.234, T.235 Ligands: GOL.35 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.235 Water bridges: D:P.231, D:T.235, D:D.236 GOL.34: 3 residues within 4Å: Chain D: R.268, D.269, I.270 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.268, D:D.269, D:I.270 GOL.35: 10 residues within 4Å: Chain D: I.229, P.231, T.235, Y.264, D.265, Q.266, P.267, A.275, R.276 Ligands: GOL.33 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.265, D:R.276 GOL.36: 3 residues within 4Å: Chain D: T.257, L.258, R.259 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.257, D:T.257 Water bridges: D:R.259, D:R.284 GOL.37: 2 residues within 4Å: Chain D: P.231, D.232 No protein-ligand interaction detected (PLIP)

14 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 7 residues within 4Å: Chain A: H.107, D.108, G.110, A.111, S.112, G.137, M.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.108, A:G.137 PEG.7: 3 residues within 4Å: Chain A: P.274, Y.275 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.274 PEG.8: 4 residues within 4Å: Chain A: A.45, Q.262, A.263 Ligands: PEG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.45 PEG.9: 5 residues within 4Å: Chain A: A.38, H.41, E.270, V.271 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.37, A:V.271 PEG.10: 7 residues within 4Å: Chain A: A.42, A.263, A.266, A.267, E.270, V.271 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.263, A:A.267 PEG.18: 6 residues within 4Å: Chain B: V.162, P.163, P.230, D.232, A.233, D.234 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.234 PEG.19: 5 residues within 4Å: Chain B: S.96, P.180, G.181, A.184 Ligands: NAD.11 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.96, B:S.96 PEG.26: 7 residues within 4Å: Chain C: H.107, D.108, G.110, A.111, S.112, G.137, M.138 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.108, C:G.137 PEG.27: 3 residues within 4Å: Chain C: P.274, Y.275 Ligands: PEG.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.274 PEG.28: 4 residues within 4Å: Chain C: A.45, Q.262, A.263 Ligands: PEG.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.45 PEG.29: 5 residues within 4Å: Chain C: A.38, H.41, E.270, V.271 Ligands: PEG.27 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.37, C:V.271 PEG.30: 7 residues within 4Å: Chain C: A.42, A.263, A.266, A.267, E.270, V.271 Ligands: PEG.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.263, C:A.267, C:E.270 PEG.38: 6 residues within 4Å: Chain D: V.162, P.163, P.230, D.232, A.233, D.234 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.234 PEG.39: 5 residues within 4Å: Chain D: S.96, P.180, G.181, A.184 Ligands: NAD.31 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.96, D:S.96

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

NAD.11: 29 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, L.117, T.118, P.119, C.146, S.177, A.178, G.179, P.180, G.181, T.182, N.185, N.296, L.297, M.300 Ligands: PEG.19 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.34, B:I.34, B:M.300 Hydrogen bonds: B:P.31, B:N.33, B:N.33, B:I.34, B:S.60, B:T.95, B:S.177, B:G.179, B:G.181, B:T.182, B:T.182, B:N.185, B:N.185, B:N.296 Water bridges: B:G.32, B:N.33, B:G.35, B:S.60, B:N.103, B:N.103 NAD.31: 29 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, S.177, A.178, G.179, P.180, G.181, T.182, N.185, N.296, L.297, M.300 Ligands: PEG.39 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.34, D:I.34, D:M.300 Hydrogen bonds: D:P.31, D:N.33, D:N.33, D:I.34, D:S.60, D:T.95, D:S.177, D:G.179, D:G.181, D:T.182, D:T.182, D:N.185, D:N.185, D:N.296 Water bridges: D:G.32, D:N.33, D:G.35, D:S.60, D:N.103, D:N.103

2 x FOR: FORMYL GROUP(Non-covalent)

FOR.20: 3 residues within 4Å: Chain A: H.119 Chain B: I.211, L.212 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:H.119 Hydrogen bonds: B:L.212 FOR.40: 3 residues within 4Å: Chain C: H.119 Chain D: I.211, L.212 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:H.119 Hydrogen bonds: D:L.212

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
A

B
B

D
B

4-hydroxy-2-oxovalerate aldolase

Acetaldehyde dehydrogenase

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