SMTL ID : 5u2k.1

Crystal structure of Galactoside O-acetyltransferase complex with CoA (H3 space group)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-trimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: K.165, D.166, I.167, C.178, K.179, V.180 Ligands: PO4.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.180 Water bridges: A:V.180 EDO.2: 4 residues within 4Å: Chain A: K.4, Y.20, Q.55, W.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.4, A:Q.55 Water bridges: A:K.4, A:Q.55, A:W.73 EDO.3: 1 residues within 4Å: Chain A: W.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.12 EDO.4: 5 residues within 4Å: Chain A: T.113, K.127, A.128, G.129, P.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.147 EDO.5: 7 residues within 4Å: Chain A: K.29, C.32, N.36, F.67, D.68 Chain C: I.65, T.85 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.29, A:N.36, A:F.67, C:T.85 EDO.9: 7 residues within 4Å: Chain B: K.165, D.166, I.167, C.178, K.179, V.180 Ligands: PO4.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.180 Water bridges: B:V.180 EDO.10: 4 residues within 4Å: Chain B: K.4, Y.20, Q.55, W.73 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.4, B:Q.55 Water bridges: B:K.4, B:Q.55, B:W.73 EDO.11: 1 residues within 4Å: Chain B: W.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.12 EDO.12: 5 residues within 4Å: Chain B: T.113, K.127, A.128, G.129, P.147 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.147 EDO.13: 7 residues within 4Å: Chain A: I.65, T.85 Chain B: K.29, C.32, N.36, F.67, D.68 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.29, B:N.36, B:F.67, A:T.85 EDO.17: 7 residues within 4Å: Chain C: K.165, D.166, I.167, C.178, K.179, V.180 Ligands: PO4.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.180 Water bridges: C:V.180 EDO.18: 4 residues within 4Å: Chain C: K.4, Y.20, Q.55, W.73 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.4, C:Q.55 Water bridges: C:K.4, C:Q.55, C:W.73 EDO.19: 1 residues within 4Å: Chain C: W.12 1 PLIP interactions: 1 interactions with chain C Water bridges: C:W.12 EDO.20: 5 residues within 4Å: Chain C: T.113, K.127, A.128, G.129, P.147 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.147 EDO.21: 7 residues within 4Å: Chain B: I.65, T.85 Chain C: K.29, C.32, N.36, F.67, D.68 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.29, C:N.36, C:F.67, B:T.85

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain C: N.84, G.104, P.105 Ligands: COA.8 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: N.84, G.104, P.105 Ligands: COA.16 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: N.84, G.104, P.105 Ligands: COA.24 Ligand excluded by PLIP

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

PO4.7: 3 residues within 4Å: Chain A: K.165, K.179 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.165, A:K.179 PO4.15: 3 residues within 4Å: Chain B: K.165, K.179 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.165, B:K.179 PO4.23: 3 residues within 4Å: Chain C: K.165, K.179 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.165, C:K.179

3 x COA: COENZYME A(Non-covalent)

COA.8: 19 residues within 4Å: Chain A: M.90, Y.110, A.112, H.114, L.146, P.147, V.162, T.164, K.165, N.176 Chain C: W.138, G.140, G.141, G.158, A.159, L.172, V.174, R.182 Ligands: CL.6 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:L.172, C:V.174 Hydrogen bonds: C:G.141, C:A.159, C:A.159, A:A.112, A:T.164, A:T.164 Water bridges: C:G.175, C:G.175 Salt bridges: C:R.182, A:K.165, A:K.179 COA.16: 19 residues within 4Å: Chain A: W.138, G.140, G.141, G.158, A.159, L.172, V.174, R.182 Chain B: M.90, Y.110, A.112, H.114, L.146, P.147, V.162, T.164, K.165, N.176 Ligands: CL.14 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.172, A:V.174 Hydrogen bonds: A:G.141, A:A.159, A:A.159, B:A.112, B:T.164, B:T.164 Water bridges: A:G.175, A:G.175 Salt bridges: A:R.182, B:K.165, B:K.179 COA.24: 19 residues within 4Å: Chain B: W.138, G.140, G.141, G.158, A.159, L.172, V.174, R.182 Chain C: M.90, Y.110, A.112, H.114, L.146, P.147, V.162, T.164, K.165, N.176 Ligands: CL.22 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:A.112, C:T.164, C:T.164, B:G.141, B:A.159, B:A.159 Salt bridges: C:K.165, C:K.179, B:R.182 Hydrophobic interactions: B:L.172, B:V.174 Water bridges: B:G.175, B:G.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czub, M.P. et al., Crystal structure of Galactoside O-acetyltransferase complexwith CoA (H3 space group). to be published

Release Date

2016-12-14

Peptides

Galactoside O-acetyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Galactoside O-acetyltransferase

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