SMTL ID : 6c7l.1

Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in a tetragonal crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x ATR: 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ATR.1: 24 residues within 4Å: Chain A: S.33, G.34, S.35, M.36, R.38, H.39, F.41, A.64, G.91, G.92, S.93, V.94, S.139, T.140, A.143, L.178, P.179, T.181, M.182, P.183, V.186 Ligands: PO4.5, PO4.7, PO4.15 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.35, A:S.35, A:G.91, A:G.92, A:S.93, A:S.139, A:S.139, A:T.140 Water bridges: A:S.33, A:G.34, A:G.34, A:R.38, A:R.38, A:R.38, A:R.38, A:T.140, A:A.143, A:H.272, A:H.272 Salt bridges: A:R.38 ATR.23: 24 residues within 4Å: Chain B: S.33, G.34, S.35, M.36, R.38, H.39, F.41, A.64, G.91, G.92, S.93, V.94, S.139, T.140, A.143, L.178, P.179, T.181, M.182, P.183, V.186 Ligands: PO4.27, PO4.29, PO4.37 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:S.35, B:S.35, B:G.91, B:G.92, B:S.93, B:S.139, B:S.139, B:T.140 Water bridges: B:S.33, B:G.34, B:G.34, B:R.38, B:R.38, B:R.38, B:R.38, B:T.140, B:A.143, B:H.272, B:H.272 Salt bridges: B:R.38

38 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: A.143, D.193, H.197, L.256, H.260, H.264, H.272, N.276 Ligand excluded by PLIP PO4.3: 7 residues within 4Å: Chain A: K.217, R.239 Chain B: P.209, D.212, R.297 Ligands: PO4.8, PO4.26 Ligand excluded by PLIP PO4.4: 5 residues within 4Å: Chain A: R.296, R.297, E.300 Chain B: R.239 Ligands: PO4.25 Ligand excluded by PLIP PO4.5: 5 residues within 4Å: Chain A: G.34, S.35, R.38, G.61 Ligands: ATR.1 Ligand excluded by PLIP PO4.6: 8 residues within 4Å: Chain A: N.161, H.260, A.261, H.264, K.265, D.352, L.354 Ligands: PO4.17 Ligand excluded by PLIP PO4.7: 8 residues within 4Å: Chain A: G.91, G.92, S.93, T.140, G.142, A.143, S.190 Ligands: ATR.1 Ligand excluded by PLIP PO4.8: 8 residues within 4Å: Chain A: K.217, K.220, T.221, R.224, W.225, R.239 Ligands: PO4.3, PO4.9 Ligand excluded by PLIP PO4.9: 3 residues within 4Å: Chain A: K.220, R.224 Ligands: PO4.8 Ligand excluded by PLIP PO4.10: 6 residues within 4Å: Chain A: I.59, G.61, L.62, P.63, V.70, F.74 Ligand excluded by PLIP PO4.11: 6 residues within 4Å: Chain A: M.1 Chain B: I.9, E.10, R.17, R.20 Ligands: PO4.12 Ligand excluded by PLIP PO4.12: 4 residues within 4Å: Chain A: M.1 Chain B: R.17, R.20 Ligands: PO4.11 Ligand excluded by PLIP PO4.13: 5 residues within 4Å: Chain A: Y.105, D.106, P.108, K.131 Ligands: PO4.14 Ligand excluded by PLIP PO4.14: 5 residues within 4Å: Chain A: Y.105, D.106, K.131, T.132 Ligands: PO4.13 Ligand excluded by PLIP PO4.15: 7 residues within 4Å: Chain A: S.35, R.38, H.39, T.181, M.182, P.183 Ligands: ATR.1 Ligand excluded by PLIP PO4.16: 4 residues within 4Å: Chain A: E.347, Y.350, H.351, P.364 Ligand excluded by PLIP PO4.17: 7 residues within 4Å: Chain A: F.117, A.150, N.161, V.163, R.255, L.354 Ligands: PO4.6 Ligand excluded by PLIP PO4.18: 4 residues within 4Å: Chain A: N.111, F.112, G.113, K.155 Ligand excluded by PLIP PO4.19: 5 residues within 4Å: Chain A: K.37, L.42, S.58, I.59, A.60 Ligand excluded by PLIP PO4.20: 4 residues within 4Å: Chain A: K.154, K.159, A.267, W.268 Ligand excluded by PLIP PO4.24: 8 residues within 4Å: Chain B: A.143, D.193, H.197, L.256, H.260, H.264, H.272, N.276 Ligand excluded by PLIP PO4.25: 7 residues within 4Å: Chain A: P.209, D.212, R.297 Chain B: K.217, R.239 Ligands: PO4.4, PO4.30 Ligand excluded by PLIP PO4.26: 5 residues within 4Å: Chain A: R.239 Chain B: R.296, R.297, E.300 Ligands: PO4.3 Ligand excluded by PLIP PO4.27: 5 residues within 4Å: Chain B: G.34, S.35, R.38, G.61 Ligands: ATR.23 Ligand excluded by PLIP PO4.28: 8 residues within 4Å: Chain B: N.161, H.260, A.261, H.264, K.265, D.352, L.354 Ligands: PO4.39 Ligand excluded by PLIP PO4.29: 8 residues within 4Å: Chain B: G.91, G.92, S.93, T.140, G.142, A.143, S.190 Ligands: ATR.23 Ligand excluded by PLIP PO4.30: 8 residues within 4Å: Chain B: K.217, K.220, T.221, R.224, W.225, R.239 Ligands: PO4.25, PO4.31 Ligand excluded by PLIP PO4.31: 3 residues within 4Å: Chain B: K.220, R.224 Ligands: PO4.30 Ligand excluded by PLIP PO4.32: 6 residues within 4Å: Chain B: I.59, G.61, L.62, P.63, V.70, F.74 Ligand excluded by PLIP PO4.33: 6 residues within 4Å: Chain A: I.9, E.10, R.17, R.20 Chain B: M.1 Ligands: PO4.34 Ligand excluded by PLIP PO4.34: 4 residues within 4Å: Chain A: R.17, R.20 Chain B: M.1 Ligands: PO4.33 Ligand excluded by PLIP PO4.35: 5 residues within 4Å: Chain B: Y.105, D.106, P.108, K.131 Ligands: PO4.36 Ligand excluded by PLIP PO4.36: 5 residues within 4Å: Chain B: Y.105, D.106, K.131, T.132 Ligands: PO4.35 Ligand excluded by PLIP PO4.37: 7 residues within 4Å: Chain B: S.35, R.38, H.39, T.181, M.182, P.183 Ligands: ATR.23 Ligand excluded by PLIP PO4.38: 4 residues within 4Å: Chain B: E.347, Y.350, H.351, P.364 Ligand excluded by PLIP PO4.39: 7 residues within 4Å: Chain B: F.117, A.150, N.161, V.163, R.255, L.354 Ligands: PO4.28 Ligand excluded by PLIP PO4.40: 4 residues within 4Å: Chain B: N.111, F.112, G.113, K.155 Ligand excluded by PLIP PO4.41: 5 residues within 4Å: Chain B: K.37, L.42, S.58, I.59, A.60 Ligand excluded by PLIP PO4.42: 4 residues within 4Å: Chain B: K.154, K.159, A.267, W.268 Ligand excluded by PLIP

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

EDO.21: 3 residues within 4Å: Chain A: R.17, S.19, R.20 No protein-ligand interaction detected (PLIP) EDO.43: 3 residues within 4Å: Chain B: R.17, S.19, R.20 No protein-ligand interaction detected (PLIP)

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.22: 5 residues within 4Å: Chain A: F.307, D.312, E.315, V.316, E.319 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.315 Hydrogen bonds: A:D.312 MPD.44: 5 residues within 4Å: Chain B: F.307, D.312, E.315, V.316, E.319 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.315 Hydrogen bonds: B:D.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larson, S.B. et al., The structure of an iron-containing alcohol dehydrogenase from a hyperthermophilic archaeon in two chemical states. Acta Crystallogr F Struct Biol Commun (2019)

Release Date

2019-02-06

Peptides

Alcohol dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alcohol dehydrogenase

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