SMTL ID : 5j78.1

Crystal structure of an Acetylating Aldehyde Dehydrogenase from Geobacillus thermoglucosidasius

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 10 residues within 4Å: Chain A: N.142, I.272, C.273, A.274, H.394, I.429, S.438, L.439, T.440, L.441 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.274 Water bridges: A:H.394 Salt bridges: A:H.394 ACT.5: 10 residues within 4Å: Chain A: A.77, A.80, K.92, K.95, N.96, T.141, N.142, P.143, T.144, S.145 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.92 Hydrogen bonds: A:N.96, A:T.144, A:S.145, A:S.145 Salt bridges: A:K.92, A:K.95 ACT.12: 10 residues within 4Å: Chain B: N.142, I.272, C.273, A.274, H.394, I.429, S.438, L.439, T.440, L.441 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.274 Water bridges: B:N.142, B:H.394 Salt bridges: B:H.394 ACT.16: 10 residues within 4Å: Chain B: A.77, A.80, K.92, K.95, N.96, T.141, N.142, P.143, T.144, S.145 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.80, B:K.92, B:P.143 Hydrogen bonds: B:T.144, B:T.144, B:S.145, B:S.145 Salt bridges: B:K.92, B:K.95 ACT.24: 9 residues within 4Å: Chain C: N.142, I.272, C.273, A.274, H.394, I.429, S.438, L.439, L.441 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.274 Water bridges: C:H.394, C:L.439 Salt bridges: C:H.394 ACT.28: 10 residues within 4Å: Chain C: A.77, A.80, K.92, K.95, N.96, T.141, N.142, P.143, T.144, S.145 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:K.92 Hydrogen bonds: C:T.144, C:S.145, C:S.145, C:D.268 Salt bridges: C:K.92, C:K.95 ACT.38: 9 residues within 4Å: Chain D: N.142, I.272, C.273, A.274, H.394, I.429, L.439, T.440, L.441 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.274 Water bridges: D:H.394, D:L.439, D:L.441 Salt bridges: D:H.394 ACT.40: 11 residues within 4Å: Chain D: A.77, A.80, K.92, K.95, N.96, T.141, N.142, P.143, T.144, S.145, T.146 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:K.92 Hydrogen bonds: D:T.144, D:T.144, D:S.145, D:S.145 Salt bridges: D:K.92, D:K.95

35 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: P.139, T.141, T.220, G.221, G.222, V.239, T.271, C.273, L.364 Ligands: GOL.3 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: F.86, S.140, T.141, H.166, L.319, A.321, V.324, L.364 Ligands: GOL.2 Ligand excluded by PLIP GOL.6: 11 residues within 4Å: Chain A: E.51, V.113, G.114, I.127, A.128, Q.129, P.130, R.158, K.464 Chain B: I.411, D.412 Ligand excluded by PLIP GOL.7: 9 residues within 4Å: Chain A: F.98, D.102, A.431, T.432 Chain B: R.471, E.472, M.473, P.474 Ligands: GOL.8 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: L.94, L.97, F.98, N.101, D.102 Chain B: M.473, P.474 Ligands: GOL.7 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: Q.47, E.51, Q.129, P.130, G.132 Chain B: I.446 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: Y.237, I.450, T.451, D.453, H.459 Chain B: Y.237, I.450, T.451, H.459 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: R.118, E.120, R.123, W.125, F.468 Chain B: E.403 Ligand excluded by PLIP GOL.13: 10 residues within 4Å: Chain B: P.139, S.140, T.141, T.220, G.221, G.222, V.239, C.273, L.364 Ligands: GOL.14 Ligand excluded by PLIP GOL.14: 9 residues within 4Å: Chain B: F.86, S.140, T.141, H.166, L.319, A.321, V.324, L.364 Ligands: GOL.13 Ligand excluded by PLIP GOL.17: 11 residues within 4Å: Chain A: I.411, D.412 Chain B: E.51, V.113, G.114, I.127, A.128, Q.129, P.130, R.158, K.464 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain A: R.471, E.472, M.473, P.474 Chain B: F.98, D.102, A.431, T.432 Ligands: GOL.19 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain A: M.473, P.474 Chain B: L.94, L.97, F.98, N.101, D.102, A.431 Ligands: GOL.18 Ligand excluded by PLIP GOL.20: 12 residues within 4Å: Chain A: I.446 Chain B: K.44, Q.47, K.48, E.51, Q.129, P.130, V.131, G.132, I.133, D.215 Ligands: MG.15 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain A: V.477 Chain B: R.70, E.71, E.72, A.73, G.74, R.75, T.93, L.97 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: K.286, V.290, K.294, F.300, E.349 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain B: I.33, R.37, E.207 Chain D: D.29, L.30, I.33, A.203 Ligands: GOL.46 Ligand excluded by PLIP GOL.25: 10 residues within 4Å: Chain C: P.139, S.140, T.141, T.220, G.221, G.222, V.239, C.273, L.364 Ligands: GOL.26 Ligand excluded by PLIP GOL.26: 9 residues within 4Å: Chain C: F.86, S.140, T.141, H.166, L.319, A.321, V.324, L.364 Ligands: GOL.25 Ligand excluded by PLIP GOL.29: 11 residues within 4Å: Chain C: E.51, V.113, G.114, I.127, A.128, Q.129, P.130, R.158, K.464 Chain D: I.411, D.412 Ligand excluded by PLIP GOL.30: 10 residues within 4Å: Chain C: F.98, D.102, A.431, T.432 Chain D: R.471, E.472, M.473, P.474 Ligands: GOL.31, GOL.32 Ligand excluded by PLIP GOL.31: 10 residues within 4Å: Chain C: L.94, L.97, F.98, N.101, D.102, A.431 Chain D: M.473, P.474 Ligands: GOL.30, GOL.32 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain C: N.101, D.102, N.105 Chain D: R.471 Ligands: GOL.30, GOL.31 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain C: R.471, E.472, M.473, P.474 Chain D: F.98, D.102, A.431, T.432 Ligands: GOL.42 Ligand excluded by PLIP GOL.34: 9 residues within 4Å: Chain C: Q.47, E.51, Q.129, P.130, V.131, G.132, D.215 Chain D: I.446 Ligands: MG.27 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain C: R.118, D.119, E.120, R.123, V.124, W.125, F.468 Chain D: E.403 Ligand excluded by PLIP GOL.36: 9 residues within 4Å: Chain C: Y.237, I.450, T.451, D.453, H.459 Chain D: Y.237, I.450, T.451, H.459 Ligand excluded by PLIP GOL.37: 8 residues within 4Å: Chain A: D.29, L.30, I.33, A.203 Chain C: I.33, R.37, N.206, E.207 Ligand excluded by PLIP GOL.41: 11 residues within 4Å: Chain C: I.411, D.412 Chain D: E.51, V.113, G.114, I.127, A.128, Q.129, P.130, R.158, K.464 Ligand excluded by PLIP GOL.42: 9 residues within 4Å: Chain C: M.473, P.474 Chain D: L.94, L.97, F.98, N.101, D.102, A.431 Ligands: GOL.33 Ligand excluded by PLIP GOL.43: 10 residues within 4Å: Chain C: I.446 Chain D: Q.47, E.51, Q.129, P.130, V.131, G.132, I.133, D.215 Ligands: MG.39 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain D: V.290, K.294, F.300, E.349 Ligand excluded by PLIP GOL.45: 7 residues within 4Å: Chain C: E.403 Chain D: D.119, E.120, R.123, W.125, F.468 Ligands: GOL.47 Ligand excluded by PLIP GOL.46: 9 residues within 4Å: Chain B: D.29, L.30, I.33, A.203 Chain D: I.33, R.37, N.206, E.207 Ligands: GOL.23 Ligand excluded by PLIP GOL.47: 7 residues within 4Å: Chain C: E.403, E.407 Chain D: I.115, R.118, E.120, W.125 Ligands: GOL.45 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: K.212, D.215 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.215, H2O.3, H2O.5 MG.15: 4 residues within 4Å: Chain B: K.212, L.213, D.215 Ligands: GOL.20 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.215, H2O.15, H2O.16, H2O.17, H2O.19 MG.27: 4 residues within 4Å: Chain C: K.212, L.213, D.215 Ligands: GOL.34 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.215, H2O.26, H2O.27, H2O.30, H2O.30 MG.39: 3 residues within 4Å: Chain D: L.213, D.215 Ligands: GOL.43 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.215, H2O.38, H2O.38, H2O.41, H2O.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Extance, J. et al., Structure of an acetylating aldehyde dehydrogenase from the thermophilic ethanologen Geobacillus thermoglucosidasius. Protein Sci. (2016)

Release Date

2016-09-07

Peptides

Acetaldehyde dehydrogenase (Acetylating): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acetaldehyde dehydrogenase (Acetylating)

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