SMTL ID : 4caz.1

CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM Pseudomonas aeruginosa IN COMPLEX WITH NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: R.70, R.74, D.77 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: F.331, R.357 Ligands: EDO.4 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: M.276, F.280, V.285, G.445 Ligands: PE4.21 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: F.331, P.332, E.335 Ligands: EDO.2 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: I.123, R.140, P.142, A.169 Ligands: EDO.16, GOL.32 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: P.263, H.295, S.297 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: R.43, W.215, E.218 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: E.126, R.140 Chain C: L.467, T.468 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: D.423, A.425, R.426 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: E.85, A.88 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Q.299, A.300, E.303, R.350 Ligands: EDO.37 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: D.317, D.320 Ligands: GOL.26 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: N.31, D.317 Ligands: GOL.34 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: A.265, D.266, L.267, R.301 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: E.248, R.475 Chain C: G.455, Y.456, G.460, V.461, G.462, R.463 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: A.65, V.120, P.121, I.123 Chain B: E.450 Chain D: I.128, P.129 Ligands: EDO.5, GOL.32 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: R.139 Chain C: H.432 Chain D: P.129, R.131, E.132 Ligands: GOL.32 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: D.379, D.380, R.385, D.410 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: F.262, E.401, D.402, I.405, R.426, R.433 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: A.265, D.266, R.269, V.420, T.421, Q.422, N.442 Ligand excluded by PLIP EDO.37: 2 residues within 4Å: Chain A: A.300 Ligands: EDO.11 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: R.14, V.16, E.17, R.48 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain B: E.446, P.448 Chain D: R.131 Ligands: EDO.42, PE4.52, GOL.59 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: I.123, R.140, P.142, A.169 Chain C: P.129 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain B: D.266, L.267, D.268, R.301, K.305 Ligand excluded by PLIP EDO.42: 8 residues within 4Å: Chain B: T.108, G.445, E.446, S.447 Ligands: EDO.39, PE4.52, K.55, GOL.58 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: F.4, Q.7, K.187 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain B: R.131, T.133, E.482, D.485 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain B: A.300, E.303, R.350 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain B: R.406, N.409, R.433 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain B: T.231, E.412, Y.413, Q.458 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain B: F.262, E.401, D.402, R.433 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain B: D.266, D.268, R.269 Ligand excluded by PLIP EDO.50: 1 residues within 4Å: Chain B: D.84 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain B: W.161, E.252, L.415 Ligands: GOL.58, TXE.61 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain C: R.70, R.74, D.77 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain C: F.331, R.357 Ligands: EDO.65 Ligand excluded by PLIP EDO.64: 5 residues within 4Å: Chain C: M.276, F.280, V.285, G.445 Ligands: PE4.82 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain C: F.331, P.332, E.335 Ligands: EDO.63 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain C: I.123, R.140, P.142, A.169 Ligands: EDO.77, GOL.93 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain C: P.263, H.295, S.297 Ligand excluded by PLIP EDO.68: 3 residues within 4Å: Chain C: R.43, W.215, E.218 Ligand excluded by PLIP EDO.69: 4 residues within 4Å: Chain A: L.467, T.468 Chain C: E.126, R.140 Ligand excluded by PLIP EDO.70: 3 residues within 4Å: Chain C: D.423, A.425, R.426 Ligand excluded by PLIP EDO.71: 2 residues within 4Å: Chain C: E.85, A.88 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain C: Q.299, A.300, E.303, R.350 Ligands: EDO.98 Ligand excluded by PLIP EDO.73: 3 residues within 4Å: Chain C: D.317, D.320 Ligands: GOL.87 Ligand excluded by PLIP EDO.74: 3 residues within 4Å: Chain C: N.31, D.317 Ligands: GOL.95 Ligand excluded by PLIP EDO.75: 4 residues within 4Å: Chain C: A.265, D.266, L.267, R.301 Ligand excluded by PLIP EDO.76: 8 residues within 4Å: Chain A: G.455, Y.456, G.460, V.461, G.462, R.463 Chain C: E.248, R.475 Ligand excluded by PLIP EDO.77: 9 residues within 4Å: Chain B: I.128, P.129 Chain C: A.65, V.120, P.121, I.123 Chain D: E.450 Ligands: EDO.66, GOL.93 Ligand excluded by PLIP EDO.78: 6 residues within 4Å: Chain A: H.432 Chain B: P.129, R.131, E.132 Chain C: R.139 Ligands: GOL.93 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain C: D.379, D.380, R.385, D.410 Ligand excluded by PLIP EDO.80: 6 residues within 4Å: Chain C: F.262, E.401, D.402, I.405, R.426, R.433 Ligand excluded by PLIP EDO.81: 7 residues within 4Å: Chain C: A.265, D.266, R.269, V.420, T.421, Q.422, N.442 Ligand excluded by PLIP EDO.98: 2 residues within 4Å: Chain C: A.300 Ligands: EDO.72 Ligand excluded by PLIP EDO.99: 4 residues within 4Å: Chain D: R.14, V.16, E.17, R.48 Ligand excluded by PLIP EDO.100: 6 residues within 4Å: Chain B: R.131 Chain D: E.446, P.448 Ligands: EDO.103, PE4.113, GOL.120 Ligand excluded by PLIP EDO.101: 5 residues within 4Å: Chain A: P.129 Chain D: I.123, R.140, P.142, A.169 Ligand excluded by PLIP EDO.102: 5 residues within 4Å: Chain D: D.266, L.267, D.268, R.301, K.305 Ligand excluded by PLIP EDO.103: 8 residues within 4Å: Chain D: T.108, G.445, E.446, S.447 Ligands: EDO.100, PE4.113, K.116, GOL.119 Ligand excluded by PLIP EDO.104: 3 residues within 4Å: Chain D: F.4, Q.7, K.187 Ligand excluded by PLIP EDO.105: 4 residues within 4Å: Chain D: R.131, T.133, E.482, D.485 Ligand excluded by PLIP EDO.106: 3 residues within 4Å: Chain D: A.300, E.303, R.350 Ligand excluded by PLIP EDO.107: 3 residues within 4Å: Chain D: R.406, N.409, R.433 Ligand excluded by PLIP EDO.108: 4 residues within 4Å: Chain D: T.231, E.412, Y.413, Q.458 Ligand excluded by PLIP EDO.109: 4 residues within 4Å: Chain D: F.262, E.401, D.402, R.433 Ligand excluded by PLIP EDO.110: 3 residues within 4Å: Chain D: D.266, D.268, R.269 Ligand excluded by PLIP EDO.111: 1 residues within 4Å: Chain D: D.84 Ligand excluded by PLIP EDO.112: 5 residues within 4Å: Chain D: W.161, E.252, L.415 Ligands: GOL.119, TXE.122 Ligand excluded by PLIP

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

PE4.21: 10 residues within 4Å: Chain A: S.103, V.104, M.276, W.444, E.446 Chain C: Y.486, A.487, V.489 Ligands: EDO.3, K.24 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:S.103, A:E.446, C:A.487 PE4.52: 11 residues within 4Å: Chain B: S.103, V.104, M.276, W.444, E.446 Chain D: Y.486, A.487, V.489 Ligands: EDO.39, EDO.42, K.55 No protein-ligand interaction detected (PLIP) PE4.82: 10 residues within 4Å: Chain A: Y.486, A.487, V.489 Chain C: S.103, V.104, M.276, W.444, E.446 Ligands: EDO.64, K.85 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:A.487, C:S.103 PE4.113: 11 residues within 4Å: Chain B: Y.486, A.487, V.489 Chain D: S.103, V.104, M.276, W.444, E.446 Ligands: EDO.100, EDO.103, K.116 No protein-ligand interaction detected (PLIP)

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

K.22: 4 residues within 4Å: Chain A: T.26, I.27, D.93, V.180 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.26, A:I.27, A:D.93, A:D.93, A:V.180 K.23: 6 residues within 4Å: Chain A: E.223, L.246, E.248 Chain C: K.457, G.460, V.461 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:K.457, C:G.460, A:L.246, A:E.248 K.24: 1 residues within 4Å: Ligands: PE4.21 No protein-ligand interaction detected (PLIP) K.53: 4 residues within 4Å: Chain B: T.26, I.27, D.93, V.180 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.26, B:I.27, B:D.93, B:D.93, B:V.180 K.54: 6 residues within 4Å: Chain B: E.223, L.246, E.248 Chain D: K.457, G.460, V.461 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:K.457, D:G.460, B:L.246, B:E.248 K.55: 2 residues within 4Å: Ligands: EDO.42, PE4.52 No protein-ligand interaction detected (PLIP) K.83: 4 residues within 4Å: Chain C: T.26, I.27, D.93, V.180 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.26, C:I.27, C:D.93, C:D.93, C:V.180 K.84: 6 residues within 4Å: Chain A: K.457, G.460, V.461 Chain C: E.223, L.246, E.248 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:K.457, A:G.460, C:L.246, C:E.248 K.85: 1 residues within 4Å: Ligands: PE4.82 No protein-ligand interaction detected (PLIP) K.114: 4 residues within 4Å: Chain D: T.26, I.27, D.93, V.180 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:T.26, D:I.27, D:D.93, D:D.93, D:V.180 K.115: 6 residues within 4Å: Chain B: K.457, G.460, V.461 Chain D: E.223, L.246, E.248 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:L.246, D:E.248, B:K.457, B:G.460 K.116: 2 residues within 4Å: Ligands: EDO.103, PE4.113 No protein-ligand interaction detected (PLIP)

32 x GOL: GLYCEROL(Non-functional Binders)

GOL.25: 3 residues within 4Å: Chain A: S.336, G.339, Y.340 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain A: L.315, G.316, D.317, D.320, N.322, T.323 Ligands: EDO.12 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain A: Q.347, R.378, D.380, M.381 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain A: E.5, E.6, Q.7, K.8, Y.15, K.187 Ligands: GOL.29 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain A: F.4, E.5, Q.7, K.187 Ligands: GOL.28 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain A: R.139, E.141, R.475, K.477 Chain C: H.432, R.433, L.434, E.435 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain A: G.13, R.14, T.193, D.199 Ligand excluded by PLIP GOL.32: 10 residues within 4Å: Chain A: A.61, M.63, A.65, R.68 Chain D: L.130, R.131, E.132 Ligands: EDO.5, EDO.16, EDO.17 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain A: W.161, E.252, T.287, L.415, V.453, E.464 Ligands: GOL.35, TXE.36 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain A: A.30, D.317, A.362, F.363, Y.368 Ligands: EDO.13 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain A: Y.154, Q.157, W.161 Ligands: GOL.33 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain B: S.336, G.339, Y.340, T.382 Ligand excluded by PLIP GOL.57: 5 residues within 4Å: Chain B: E.5, E.6, Q.7, K.8, Y.15 Ligand excluded by PLIP GOL.58: 5 residues within 4Å: Chain B: Y.154, Q.157, T.287 Ligands: EDO.42, EDO.51 Ligand excluded by PLIP GOL.59: 5 residues within 4Å: Chain B: D.111, P.448, A.449, E.450 Ligands: EDO.39 Ligand excluded by PLIP GOL.60: 5 residues within 4Å: Chain B: A.30, D.317, A.362, F.363, Y.368 Ligand excluded by PLIP GOL.86: 3 residues within 4Å: Chain C: S.336, G.339, Y.340 Ligand excluded by PLIP GOL.87: 7 residues within 4Å: Chain C: L.315, G.316, D.317, D.320, N.322, T.323 Ligands: EDO.73 Ligand excluded by PLIP GOL.88: 4 residues within 4Å: Chain C: Q.347, R.378, D.380, M.381 Ligand excluded by PLIP GOL.89: 7 residues within 4Å: Chain C: E.5, E.6, Q.7, K.8, Y.15, K.187 Ligands: GOL.90 Ligand excluded by PLIP GOL.90: 5 residues within 4Å: Chain C: F.4, E.5, Q.7, K.187 Ligands: GOL.89 Ligand excluded by PLIP GOL.91: 8 residues within 4Å: Chain A: H.432, R.433, L.434, E.435 Chain C: R.139, E.141, R.475, K.477 Ligand excluded by PLIP GOL.92: 4 residues within 4Å: Chain C: G.13, R.14, T.193, D.199 Ligand excluded by PLIP GOL.93: 10 residues within 4Å: Chain B: L.130, R.131, E.132 Chain C: A.61, M.63, A.65, R.68 Ligands: EDO.66, EDO.77, EDO.78 Ligand excluded by PLIP GOL.94: 8 residues within 4Å: Chain C: W.161, E.252, T.287, L.415, V.453, E.464 Ligands: GOL.96, TXE.97 Ligand excluded by PLIP GOL.95: 6 residues within 4Å: Chain C: A.30, D.317, A.362, F.363, Y.368 Ligands: EDO.74 Ligand excluded by PLIP GOL.96: 4 residues within 4Å: Chain C: Y.154, Q.157, W.161 Ligands: GOL.94 Ligand excluded by PLIP GOL.117: 4 residues within 4Å: Chain D: S.336, G.339, Y.340, T.382 Ligand excluded by PLIP GOL.118: 5 residues within 4Å: Chain D: E.5, E.6, Q.7, K.8, Y.15 Ligand excluded by PLIP GOL.119: 5 residues within 4Å: Chain D: Y.154, Q.157, T.287 Ligands: EDO.103, EDO.112 Ligand excluded by PLIP GOL.120: 5 residues within 4Å: Chain D: D.111, P.448, A.449, E.450 Ligands: EDO.100 Ligand excluded by PLIP GOL.121: 5 residues within 4Å: Chain D: A.30, D.317, A.362, F.363, Y.368 Ligand excluded by PLIP

4 x TXE: [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate(Covalent)

TXE.36: 25 residues within 4Å: Chain A: I.149, G.150, A.151, W.152, N.153, K.176, P.177, S.178, E.179, G.209, G.213, Q.214, F.227, T.228, G.229, G.230, T.233, V.237, E.252, L.253, G.254, C.286, E.387, F.389 Ligands: GOL.33 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.151, A:T.228, A:F.389 Hydrogen bonds: A:K.176, A:P.177, A:E.179, A:Q.214, A:G.230, A:E.252, A:E.387 Water bridges: A:N.153, A:T.233, A:T.233, A:E.387 TXE.61: 25 residues within 4Å: Chain B: I.149, G.150, A.151, W.152, N.153, K.176, P.177, S.178, E.179, G.209, G.213, Q.214, F.227, T.228, G.229, G.230, T.233, V.237, E.252, L.253, G.254, C.286, E.387, F.389 Ligands: EDO.51 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.151, B:T.228 Hydrogen bonds: B:K.176, B:E.179, B:G.209, B:Q.214, B:G.230, B:T.233, B:E.252, B:E.387 Water bridges: B:N.153, B:R.210, B:G.230, B:T.233 TXE.97: 25 residues within 4Å: Chain C: I.149, G.150, A.151, W.152, N.153, K.176, P.177, S.178, E.179, G.209, G.213, Q.214, F.227, T.228, G.229, G.230, T.233, V.237, E.252, L.253, G.254, C.286, E.387, F.389 Ligands: GOL.94 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.151, C:T.228, C:F.389 Hydrogen bonds: C:K.176, C:P.177, C:E.179, C:Q.214, C:G.230, C:T.233, C:E.252, C:E.387 Water bridges: C:N.153, C:T.231, C:T.233 TXE.122: 25 residues within 4Å: Chain D: I.149, G.150, A.151, W.152, N.153, K.176, P.177, S.178, E.179, G.209, G.213, Q.214, F.227, T.228, G.229, G.230, T.233, V.237, E.252, L.253, G.254, C.286, E.387, F.389 Ligands: EDO.112 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.151, D:T.228 Hydrogen bonds: D:K.176, D:E.179, D:G.209, D:Q.214, D:G.230, D:T.233, D:T.233, D:E.252, D:E.387 Water bridges: D:N.153, D:R.210, D:G.230, D:T.233

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
A

D
B

BETAINE ALDEHYDE DEHYDROGENASE

Related Entries With Identical Sequence