SMTL ID : 7r5t.1

CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F254I COMPLEXED WITH FE, NADH, AND GLYCEROL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 37 residues within 4Å: Chain A: D.39, T.41, L.42, C.45, V.47, P.70, N.71, P.72, G.97, G.98, S.99, P.100, D.102, K.105, T.140, T.141, T.144, A.146, T.149, N.151, Y.152, V.153, K.162, M.181, M.182, G.184, M.185, P.186, L.189, T.193, D.196, H.200, I.254, H.263, H.277 Ligands: APR.2, FE.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:D.39, A:T.41, A:N.71, A:N.71, A:G.97, A:G.98, A:S.99, A:S.99, A:S.99, A:D.102, A:K.105, A:T.140, A:T.141, A:T.149, A:K.162, A:M.185 Water bridges: A:N.71, A:D.102, A:T.144, A:V.153, A:V.153, A:G.184, A:G.278 NAI.8: 38 residues within 4Å: Chain B: D.39, T.41, L.42, C.45, V.47, P.70, N.71, P.72, G.97, G.98, S.99, P.100, D.102, K.105, T.140, T.141, T.144, A.146, T.149, N.151, Y.152, V.153, K.162, M.181, M.182, G.184, M.185, P.186, L.189, T.193, D.196, H.200, I.254, H.263, H.267, H.277 Ligands: APR.9, FE.11 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:T.41, B:N.71, B:G.97, B:G.98, B:S.99, B:S.99, B:S.99, B:K.105, B:T.140, B:T.141, B:T.149, B:N.151, B:K.162, B:M.185 Water bridges: B:N.71, B:D.102, B:T.144, B:V.153, B:G.184, B:G.184, B:H.267, B:G.278

2 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.2: 28 residues within 4Å: Chain A: D.39, T.41, L.42, C.45, V.47, P.70, N.71, P.72, G.97, G.98, S.99, P.100, D.102, T.140, T.141, T.144, V.153, K.162, M.181, M.182, G.184, M.185, P.186, L.189, T.193, H.277 Ligands: NAI.1, FE.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:T.41, A:T.41, A:N.71, A:N.71, A:G.97, A:G.98, A:S.99, A:S.99, A:S.99, A:T.140, A:T.141, A:K.162, A:M.185 Water bridges: A:N.71, A:D.102, A:T.144, A:V.153, A:V.153, A:G.184, A:H.277, A:H.277, A:G.278 Salt bridges: A:H.277 APR.9: 29 residues within 4Å: Chain B: D.39, T.41, L.42, C.45, V.47, P.70, N.71, P.72, G.97, G.98, S.99, P.100, D.102, T.140, T.141, T.144, V.153, K.162, M.181, M.182, G.184, M.185, P.186, L.189, T.193, H.267, H.277 Ligands: NAI.8, FE.11 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.41, B:N.71, B:G.97, B:G.98, B:S.99, B:S.99, B:S.99, B:S.99, B:T.140, B:T.141, B:K.162 Water bridges: B:D.102, B:D.102, B:T.144, B:H.267, B:H.277, B:H.277, B:G.278 Salt bridges: B:H.277

2 x FE: FE (III) ION(Non-covalent)

FE.3: 7 residues within 4Å: Chain A: D.196, H.200, H.263, H.277, N.281 Ligands: NAI.1, APR.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.196, A:H.200, A:H.263, A:H.277, H2O.1, H2O.4 FE.11: 7 residues within 4Å: Chain B: D.196, H.200, H.263, H.277, N.281 Ligands: NAI.8, APR.9 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.196, B:H.200, B:H.263, B:H.277, H2O.6, H2O.9

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.129, K.130, P.131 Chain B: R.28, R.29, G.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.29 GOL.5: 9 residues within 4Å: Chain A: I.7, P.131, P.168, H.169, I.171 Chain B: E.10, T.11, R.29 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) GOL.6: 6 residues within 4Å: Chain A: E.10, Q.173 Chain B: E.10, Q.173 Ligands: GOL.5, GOL.10 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.173, B:E.10, B:Q.173, B:Q.173 GOL.7: 4 residues within 4Å: Chain A: Q.32, G.59, L.60, A.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.59, A:A.61 Water bridges: A:A.34 GOL.10: 12 residues within 4Å: Chain B: P.131, S.132, V.133, P.134, I.135, H.169, D.170, I.171, P.172, Q.173 Ligands: GOL.6, GOL.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.135, B:I.135, B:Q.173, B:Q.173 Water bridges: B:N.112, B:S.132 GOL.12: 9 residues within 4Å: Chain A: E.10, T.11, R.29 Chain B: I.7, P.131, P.168, H.169, I.171 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.11, A:R.29 Water bridges: A:E.25, A:R.29 GOL.13: 7 residues within 4Å: Chain B: V.43, G.46, V.48, A.49, T.52, W.62, I.64 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.46, B:A.49 GOL.14: 2 residues within 4Å: Chain B: D.53, D.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.56 Water bridges: B:D.56, B:D.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zavarise, A. et al., Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics. Febs J. (2023)

Release Date

2022-10-19

Peptides

Lactaldehyde reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Lactaldehyde reductase

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