SMTL ID : 4ia6.1

Hydratase from lactobacillus acidophilus in a ligand bound form (LA LAH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 10 residues within 4Å: Chain A: T.184, M.185, A.187, W.343, I.378, S.389, Y.411, A.412, L.413 Ligands: MPD.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.187, A:W.343, A:W.343, A:I.378, A:Y.411, A:Y.411 Hydrogen bonds: A:M.185 Water bridges: A:L.413

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

MPD.2: 9 residues within 4Å: Chain A: T.184, M.185, A.187, W.343, S.389, Y.411, A.412, L.413 Ligands: MRD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.187, A:W.343, A:W.343, A:W.343, A:Y.411, A:L.413 Hydrogen bonds: A:T.184 Water bridges: A:L.413 MPD.3: 11 residues within 4Å: Chain A: E.82, M.83, E.84, F.87, M.185, F.186, F.204, H.207, L.211, L.217, T.508 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.82, A:F.87, A:F.186, A:F.204, A:F.204, A:L.211, A:L.217, A:T.508 Hydrogen bonds: A:E.82, A:E.82 MPD.11: 8 residues within 4Å: Chain A: I.153, R.198, M.202, I.537, Y.538, L.543 Chain B: I.540, L.584 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.153, A:I.537, A:L.543, B:I.540, B:L.584 Hydrogen bonds: A:I.537 MPD.18: 10 residues within 4Å: Chain B: E.82, M.83, E.84, M.185, F.186, F.204, H.207, L.211, L.217, T.508 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.82, B:F.186, B:F.204, B:F.204, B:F.204, B:H.207, B:L.211, B:L.217, B:T.508 Hydrogen bonds: B:E.82, B:E.82 MPD.28: 9 residues within 4Å: Chain B: T.184, M.185, A.187, W.343, I.378, S.389, W.409, Y.411, L.413 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.343, B:W.343, B:W.409 Water bridges: B:Y.411

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: V.76, G.79, G.80, S.346, W.409, Y.411, M.465 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.76, A:G.80, A:S.346, A:Y.411, A:Y.411 Water bridges: A:G.80 GOL.5: 4 residues within 4Å: Chain A: I.307, N.309, L.338, F.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.309 Water bridges: A:Y.464, A:Y.464 GOL.6: 8 residues within 4Å: Chain A: T.502, R.503, E.532, V.533, D.535, Y.538 Chain B: R.541 Ligands: GOL.21 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.541, A:R.503, A:R.503, A:E.532, A:Y.538, A:Y.538 GOL.7: 8 residues within 4Å: Chain A: G.31, L.32, A.33, T.288, Y.471, G.495, N.496, S.512 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.32, A:A.33, A:Y.471, A:Y.471, A:N.496, A:N.496, A:S.512 Water bridges: A:G.31, A:G.31 GOL.12: 5 residues within 4Å: Chain A: Q.301, N.302, K.432, S.454, E.455 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.301, A:N.302, A:N.302, A:K.432, A:E.455 Water bridges: A:K.432 GOL.13: 5 residues within 4Å: Chain A: Y.3, S.4, N.5, E.532 Chain B: R.541 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Water bridges: B:D.539, B:R.541, B:R.541, B:R.541, B:R.541, B:Q.542, A:N.5 Hydrogen bonds: A:S.4 GOL.21: 4 residues within 4Å: Chain A: Y.3, P.501 Chain B: N.589 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.589, B:N.589 GOL.22: 5 residues within 4Å: Chain B: G.162, Q.163, T.164, E.167, R.476 No protein-ligand interaction detected (PLIP) GOL.23: 2 residues within 4Å: Chain B: I.153, M.547 No protein-ligand interaction detected (PLIP) GOL.26: 7 residues within 4Å: Chain B: G.31, L.32, A.33, Y.471, G.495, N.496, S.512 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.33, B:N.496, B:N.496, B:S.512 Water bridges: B:G.31, B:G.31, B:L.32, B:Y.471

1 x EIC: LINOLEIC ACID(Non-covalent)

EIC.8: 8 residues within 4Å: Chain A: I.149, I.153, M.154, I.205, L.543, A.546, M.547, M.550 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.149, A:I.153, A:I.205, A:A.546 Salt bridges: B:K.577

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 5 residues within 4Å: Chain A: H.206, H.207, I.208, D.209, R.545 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.205, A:D.209 NA.14: 5 residues within 4Å: Chain A: F.11, D.13 Chain B: R.95, S.106, D.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.106, B:S.106

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

PO4.10: 6 residues within 4Å: Chain A: R.95, S.96, I.97, P.98, A.105, S.106 No protein-ligand interaction detected (PLIP) PO4.16: 5 residues within 4Å: Chain A: N.129, D.383, N.420, Y.440, H.441 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.129, A:N.420, A:Y.440, A:H.441 Water bridges: A:R.130, A:D.383, A:D.383 PO4.25: 5 residues within 4Å: Chain A: R.541 Chain B: Y.3, S.4, N.5, E.532 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Water bridges: A:R.541, A:R.541, A:R.541, A:Q.542, A:Q.542, B:N.5, B:N.5 Salt bridges: A:R.541 Hydrogen bonds: B:Y.3 PO4.29: 4 residues within 4Å: Chain B: T.502, R.503, E.532, V.533 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.503, B:V.533 Water bridges: B:R.503, B:R.503, A:R.541, A:R.541, A:R.541, A:R.541 Salt bridges: B:R.503

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.15: 4 residues within 4Å: Chain A: A.18, G.19, V.20, D.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.19, A:D.21 MES.19: 4 residues within 4Å: Chain B: K.365, R.366, S.367, D.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.367 Water bridges: B:D.370 MES.20: 2 residues within 4Å: Chain B: N.420, Y.440 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.420 Water bridges: B:N.385, B:N.385, B:K.423 Salt bridges: B:K.423

2 x K: POTASSIUM ION(Non-covalent)

K.17: 5 residues within 4Å: Chain A: S.367, D.370, K.372, V.373, N.374 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.367, A:D.370, A:K.372, A:V.373, H2O.6 K.30: 5 residues within 4Å: Chain B: S.367, D.370, K.372, V.373, N.374 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.367, B:D.370, B:K.372, B:V.373, H2O.29

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.24: 6 residues within 4Å: Chain B: V.77, G.79, G.80, S.346, W.409, M.465 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.77, B:G.79, B:G.80, B:S.346, B:S.346

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.27: 1 residues within 4Å: Chain B: S.96 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volkov, A. et al., Crystal structure analysis of a fatty acid double-bond hydratase from Lactobacillus acidophilus. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-03-27

Peptides

Myosin-crossreactive antigen: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Myosin-crossreactive antigen

Related Entries With Identical Sequence