SMTL ID : 4cbb.2 (1 other biounit)

APO FORM OF BETAINE ALDEHYDE DEHYDROGENASE FROM Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.1: 7 residues within 4Å: Chain A: G.228, G.229, L.252, G.253, C.285, E.386, F.388 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.386 Water bridges: A:W.151, A:T.230, A:E.386 DTT.10: 7 residues within 4Å: Chain B: G.228, G.229, L.252, G.253, C.285, E.386, F.388 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.386 Water bridges: B:T.230 DTT.21: 7 residues within 4Å: Chain C: G.228, G.229, L.252, G.253, C.285, E.386, F.388 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.386 Water bridges: C:G.229, C:T.230 DTT.32: 8 residues within 4Å: Chain D: W.151, G.228, G.229, L.252, G.253, C.285, E.386, F.388 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.386 Water bridges: D:G.229, D:T.230

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: D.378, D.379, R.384, D.409 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.409 EDO.11: 3 residues within 4Å: Chain B: S.335, G.338, Y.339 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.335 EDO.22: 7 residues within 4Å: Chain A: L.423 Chain C: R.268, Q.421, N.441 Chain D: E.481, L.482, G.483 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:N.441, D:E.481 Water bridges: C:Q.421, A:A.424 EDO.23: 8 residues within 4Å: Chain C: W.160, E.251, C.285, T.286, L.414, I.437, V.452 Ligands: GOL.25 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.446, C:S.446 EDO.33: 5 residues within 4Å: Chain D: R.130, T.132, E.481, G.483, D.484 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.130, D:T.132, D:E.481, D:D.484 EDO.34: 5 residues within 4Å: Chain D: M.275, F.279, W.443, G.444 Ligands: PE4.35 2 PLIP interactions: 2 interactions with chain D Water bridges: D:T.286, D:N.287

4 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.3: 13 residues within 4Å: Chain A: S.102, V.103, T.107, Q.156, M.275, W.443, G.444, E.445 Chain B: Y.485, A.486, V.488 Ligands: GOL.4, K.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.107 PE4.12: 10 residues within 4Å: Chain A: Y.485, A.486, V.488 Chain B: S.102, V.103, T.107, M.275, W.443, E.445 Ligands: K.20 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.486 PE4.24: 12 residues within 4Å: Chain C: S.102, V.103, M.275, F.279, W.443, G.444, E.445 Chain D: Y.485, A.486, V.488 Ligands: GOL.25, K.31 No protein-ligand interaction detected (PLIP) PE4.35: 11 residues within 4Å: Chain C: A.486, V.488 Chain D: S.102, V.103, T.107, M.275, W.443, G.444, E.445 Ligands: EDO.34, K.40 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.445

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: Y.153, Q.156, V.284 Ligands: PE4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.156 Water bridges: A:N.152, A:T.286, A:T.286 GOL.5: 7 residues within 4Å: Chain A: A.60, A.61, M.62, R.67 Chain C: L.129, R.130, E.131 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.64, A:R.67, A:R.67, C:P.128 Water bridges: A:A.60, C:E.131 GOL.6: 6 residues within 4Å: Chain A: E.247, V.248, V.460 Chain B: E.247, V.248, V.460 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.247, B:E.247, B:V.248, A:E.247, A:V.248 Water bridges: A:G.461 GOL.13: 5 residues within 4Å: Chain B: Y.153, Q.156, W.160, V.284 Ligands: GOL.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.156 Water bridges: B:T.107, B:T.107, B:C.285, B:T.286 GOL.14: 5 residues within 4Å: Chain B: F.3, E.4, Q.6, L.88, K.186 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.4, B:E.4, B:Q.6 Water bridges: B:K.186 GOL.15: 7 residues within 4Å: Chain A: H.431, R.432, L.433, E.434 Chain B: R.138, E.140, K.476 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:L.433, B:R.138, B:K.476 Water bridges: A:E.434, B:Q.56, B:R.474 GOL.16: 4 residues within 4Å: Chain B: R.130, T.132, E.481, D.484 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.130, B:T.132, B:T.132, B:E.481, B:D.484 GOL.17: 6 residues within 4Å: Chain B: W.160, E.251, T.286, L.414, I.437 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.446, B:E.463 GOL.25: 6 residues within 4Å: Chain C: Y.153, Q.156, W.160, V.284 Ligands: EDO.23, PE4.24 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.156 Water bridges: C:N.152, C:T.286, C:S.446 GOL.26: 4 residues within 4Å: Chain C: S.335, G.338, Y.339, T.381 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.339 GOL.27: 4 residues within 4Å: Chain C: F.3, E.4, Q.6, K.186 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.4, C:Q.6, C:K.186 GOL.28: 6 residues within 4Å: Chain C: G.208, G.212, Q.213, T.216, T.232, V.236 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.212 Water bridges: C:Q.213, C:Q.213, C:T.232, C:K.235 GOL.36: 4 residues within 4Å: Chain D: Y.153, Q.156, W.160, V.284 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.156 Water bridges: D:T.107, D:T.107, D:C.285 GOL.37: 3 residues within 4Å: Chain D: F.3, Q.6, K.186 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.6, D:K.186 Water bridges: D:E.4, D:Q.6

12 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.7: 4 residues within 4Å: Chain A: T.25, I.26, D.92, V.179 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.26, A:D.92, A:D.92, A:V.179, H2O.4 K.8: 3 residues within 4Å: Chain A: K.456, G.459 Chain B: L.245 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:K.456, A:G.459, B:L.245, H2O.22, H2O.35 K.9: 1 residues within 4Å: Ligands: PE4.3 No protein-ligand interaction detected (PLIP) K.18: 4 residues within 4Å: Chain B: T.25, I.26, D.92, V.179 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.26, B:D.92, B:D.92, B:V.179, H2O.26 K.19: 4 residues within 4Å: Chain A: L.245 Chain B: K.456, G.459, V.460 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:K.456, B:G.459, A:L.245, H2O.14, H2O.15 K.20: 1 residues within 4Å: Ligands: PE4.12 No protein-ligand interaction detected (PLIP) K.29: 4 residues within 4Å: Chain C: T.25, I.26, D.92, V.179 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.26, C:D.92, C:D.92, C:V.179, H2O.44 K.30: 4 residues within 4Å: Chain C: K.456, G.459, V.460 Chain D: L.245 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:L.245, C:K.456, C:G.459, H2O.57, H2O.68 K.31: 1 residues within 4Å: Ligands: PE4.24 No protein-ligand interaction detected (PLIP) K.38: 4 residues within 4Å: Chain D: T.25, I.26, D.92, V.179 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:T.25, D:I.26, D:D.92, D:D.92, D:V.179 K.39: 5 residues within 4Å: Chain C: L.245, E.247 Chain D: K.456, G.459, V.460 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:K.456, D:G.459, C:L.245, H2O.51, H2O.52 K.40: 1 residues within 4Å: Ligands: PE4.35 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Sanchez, A.G. et al., The Structural Bases of the Dual Coenzyme Specificity of Betaine Aldehyde Dehydrogenase from Pseudomonas Aeruginosa. To be Published

Release Date

2014-10-29

Peptides

BETAINE ALDEHYDE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BETAINE ALDEHYDE DEHYDROGENASE

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