SMTL ID : 6xn8.1

Crystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospirillales bacterium URHD0017

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.441, S.442, N.468, G.470, G.472 Ligands: TZD.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.441, A:G.470, H2O.3 MG.5: 6 residues within 4Å: Chain B: D.441, S.442, N.468, G.470, G.472 Ligands: TZD.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.441, B:G.470, H2O.26 MG.9: 6 residues within 4Å: Chain C: D.441, S.442, N.468, G.470, G.472 Ligands: TZD.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.441, C:G.470, H2O.51 MG.13: 6 residues within 4Å: Chain D: D.441, S.442, N.468, G.470, G.472 Ligands: TZD.14 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.441, D:G.470, H2O.74

4 x TZD: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TZD.2: 29 residues within 4Å: Chain A: Y.367, G.388, A.389, G.390, T.391, G.414, T.415, M.416, G.440, D.441, S.442, A.443, F.446, N.468, G.470, I.471, G.472 Chain B: V.25, V.26, G.27, F.28, E.50, V.73, P.76, G.77, H.80, F.112, Q.113 Ligands: MG.1 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.471, A:I.471, B:V.73, B:P.76 Hydrogen bonds: A:Y.367, A:A.389, A:G.390, A:T.391, A:G.414, A:M.416, A:G.440, A:D.441, A:S.442, A:A.443, A:N.468, A:G.472, B:Q.113 Water bridges: A:T.391, A:N.468, B:F.28, B:V.73 TZD.6: 29 residues within 4Å: Chain A: V.25, V.26, G.27, F.28, E.50, V.73, P.76, G.77, H.80, F.112, Q.113 Chain B: Y.367, G.388, A.389, G.390, T.391, G.414, T.415, M.416, G.440, D.441, S.442, A.443, F.446, N.468, G.470, I.471, G.472 Ligands: MG.5 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.367, B:A.389, B:G.390, B:T.391, B:T.391, B:G.414, B:M.416, B:G.440, B:D.441, B:S.442, B:A.443, B:N.468, B:G.472, A:Q.113 Water bridges: B:T.391, B:T.391, A:V.73 Hydrophobic interactions: A:V.73, A:P.76 TZD.10: 29 residues within 4Å: Chain C: Y.367, G.388, A.389, G.390, T.391, G.414, T.415, M.416, G.440, D.441, S.442, A.443, F.446, N.468, G.470, I.471, G.472 Chain D: V.25, V.26, G.27, F.28, E.50, V.73, P.76, G.77, H.80, F.112, Q.113 Ligands: MG.9 21 PLIP interactions: 16 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.471, C:I.471, D:V.73, D:P.76 Hydrogen bonds: C:Y.367, C:A.389, C:G.390, C:T.391, C:G.414, C:M.416, C:G.440, C:D.441, C:S.442, C:A.443, C:N.468, C:G.472, D:Q.113 Water bridges: C:T.391, C:N.468, D:F.28, D:V.73 TZD.14: 29 residues within 4Å: Chain C: V.25, V.26, G.27, F.28, E.50, V.73, P.76, G.77, H.80, F.112, Q.113 Chain D: Y.367, G.388, A.389, G.390, T.391, G.414, T.415, M.416, G.440, D.441, S.442, A.443, F.446, N.468, G.470, I.471, G.472 Ligands: MG.13 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Y.367, D:A.389, D:G.390, D:T.391, D:T.391, D:G.414, D:M.416, D:G.440, D:D.441, D:S.442, D:A.443, D:N.468, D:G.472, C:Q.113 Water bridges: D:T.391, D:D.441, C:V.73 Hydrophobic interactions: C:V.73, C:P.76

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 25 residues within 4Å: Chain A: C.92, R.152, P.153, G.211, K.212, G.213, W.216, S.217, S.237, G.240, G.270, A.271, R.272, N.274, I.276, F.277, L.294, D.295, I.296, A.297, E.300, G.313, D.314, G.315, T.412 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:R.152, A:R.152, A:K.212, A:S.237, A:S.237, A:S.237, A:R.272, A:N.274, A:D.295, A:I.296, A:D.314, A:G.315, A:T.412, A:T.412 Water bridges: A:K.212, A:W.216, A:G.240, A:R.272, A:R.272 Salt bridges: A:K.212, A:K.212, A:R.272 ADP.7: 26 residues within 4Å: Chain B: N.91, C.92, R.152, P.153, G.211, K.212, G.213, W.216, S.217, S.237, G.240, G.270, A.271, R.272, N.274, I.276, F.277, L.294, D.295, I.296, A.297, E.300, G.313, D.314, G.315, T.412 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:R.152, B:R.152, B:K.212, B:G.213, B:S.217, B:S.237, B:S.237, B:R.272, B:N.274, B:D.295, B:I.296, B:D.314, B:D.314, B:G.315, B:T.412, B:T.412 Water bridges: B:K.212, B:K.212, B:W.216, B:S.237, B:G.240 Salt bridges: B:K.212, B:K.212, B:R.272 ADP.11: 25 residues within 4Å: Chain C: C.92, R.152, P.153, G.211, K.212, G.213, W.216, S.217, S.237, G.240, G.270, A.271, R.272, N.274, I.276, F.277, L.294, D.295, I.296, A.297, E.300, G.313, D.314, G.315, T.412 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:R.152, C:R.152, C:K.212, C:S.237, C:S.237, C:S.237, C:R.272, C:N.274, C:D.295, C:I.296, C:D.314, C:D.314, C:G.315, C:T.412, C:T.412 Water bridges: C:K.212, C:W.216, C:G.240, C:R.272, C:R.272 Salt bridges: C:K.212, C:K.212, C:R.272 ADP.15: 26 residues within 4Å: Chain D: N.91, C.92, R.152, P.153, G.211, K.212, G.213, W.216, S.217, S.237, G.240, G.270, A.271, R.272, N.274, I.276, F.277, L.294, D.295, I.296, A.297, E.300, G.313, D.314, G.315, T.412 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:R.152, D:R.152, D:K.212, D:G.213, D:S.217, D:S.237, D:S.237, D:R.272, D:N.274, D:D.295, D:I.296, D:D.314, D:G.315, D:T.412, D:T.412 Water bridges: D:K.212, D:K.212, D:W.216, D:S.237, D:G.240 Salt bridges: D:K.212, D:K.212, D:R.272

4 x UNL: UNKNOWN LIGAND

UNL.4: 10 residues within 4Å: Chain A: N.192, I.301, T.307, E.308, V.309, A.310 Chain D: Y.150, P.181, E.182, P.184 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain A Water bridges: D:R.185, A:T.307, A:T.307 Hydrogen bonds: A:N.192, A:E.308, A:A.310 UNL.8: 10 residues within 4Å: Chain B: N.192, I.301, T.307, E.308, V.309, A.310 Chain C: Y.150, P.181, E.182, P.184 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.192, B:E.308, B:A.310 Water bridges: B:T.307 UNL.12: 10 residues within 4Å: Chain B: Y.150, P.181, E.182, P.184 Chain C: N.192, I.301, T.307, E.308, V.309, A.310 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.192, C:E.308, C:A.310 Water bridges: C:T.307, C:T.307, B:R.185 UNL.16: 10 residues within 4Å: Chain A: Y.150, P.181, E.182, P.184 Chain D: N.192, I.301, T.307, E.308, V.309, A.310 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.192, D:E.308, D:A.310 Water bridges: D:T.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chou, A. et al., Crystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospirillales bacterium URHD0017. To Be Published

Release Date

2021-07-07

Peptides

2-hydroxyacyl-CoA lyase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-hydroxyacyl-CoA lyase 1