SMTL ID : 7l7y.1

x-ray structure of the N-acetyltransferase Pcryo_0637 from psychrobacter cryohalolentis in the presence of UDP and acetyl-conezyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 12 residues within 4Å: Chain A: Y.8, G.9, S.11, G.12, C.13, D.40, D.41, A.42, I.74, A.75, I.79, I.83 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.79 Hydrogen bonds: A:S.11, A:S.11, A:C.13, A:D.41, A:D.41, A:A.42, A:A.75 Water bridges: A:S.11, A:G.12, A:G.12, A:N.76 UDP.6: 12 residues within 4Å: Chain B: Y.8, G.9, S.11, G.12, C.13, D.40, D.41, A.42, I.74, A.75, I.79, I.83 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.79 Hydrogen bonds: B:S.11, B:S.11, B:C.13, B:D.41, B:D.41, B:A.42, B:A.75 Water bridges: B:S.11, B:G.12, B:G.12, B:N.76 UDP.11: 12 residues within 4Å: Chain C: Y.8, G.9, S.11, G.12, C.13, D.40, D.41, A.42, I.74, A.75, I.79, I.83 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.79 Hydrogen bonds: C:S.11, C:S.11, C:C.13, C:D.41, C:D.41, C:A.42, C:A.75 Water bridges: C:S.11, C:G.12, C:G.12, C:N.76

3 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.2: 18 residues within 4Å: Chain A: A.153, Y.169, G.171, T.172, I.192, G.194, M.195, I.210, L.217 Chain B: E.141, N.159, G.160, K.177, Q.178, V.198, T.200, N.212, P.213 24 PLIP interactions: 16 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:E.141, A:I.192, A:I.210 Hydrogen bonds: B:G.160, B:Q.178, B:T.200, B:T.200, A:Y.169, A:T.172, A:T.172, A:M.195, A:M.195 Water bridges: B:K.177, B:K.177, B:K.177, B:K.177, B:K.177, B:Q.178, B:Q.178, B:K.201, A:G.211 Salt bridges: B:K.177, B:K.177, B:K.201 ACO.7: 18 residues within 4Å: Chain B: A.153, Y.169, G.171, T.172, I.192, G.194, M.195, I.210, L.217 Chain C: E.141, N.159, G.160, K.177, Q.178, V.198, T.200, N.212, P.213 24 PLIP interactions: 8 interactions with chain B, 16 interactions with chain C Hydrophobic interactions: B:I.192, B:I.210, C:E.141 Hydrogen bonds: B:Y.169, B:T.172, B:T.172, B:M.195, B:M.195, C:G.160, C:Q.178, C:T.200, C:T.200 Water bridges: B:G.211, C:K.177, C:K.177, C:K.177, C:K.177, C:K.177, C:Q.178, C:Q.178, C:K.201 Salt bridges: C:K.177, C:K.177, C:K.201 ACO.12: 18 residues within 4Å: Chain A: E.141, N.159, G.160, K.177, Q.178, V.198, T.200, N.212, P.213 Chain C: A.153, Y.169, G.171, T.172, I.192, G.194, M.195, I.210, L.217 24 PLIP interactions: 16 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:E.141, C:I.192, C:I.210 Hydrogen bonds: A:G.160, A:Q.178, A:T.200, A:T.200, C:Y.169, C:T.172, C:T.172, C:M.195, C:M.195 Water bridges: A:K.177, A:K.177, A:K.177, A:K.177, A:K.177, A:Q.178, A:Q.178, A:K.201, C:G.211 Salt bridges: A:K.177, A:K.177, A:K.201

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

MPD.3: 4 residues within 4Å: Chain A: Q.35, V.37, T.53, I.63 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.53, A:I.63 Hydrogen bonds: A:Q.35 Water bridges: A:T.53, A:T.53 MPD.4: 6 residues within 4Å: Chain A: G.173 Chain B: G.173, V.175 Chain C: G.173 Ligands: MPD.9, MPD.14 No protein-ligand interaction detected (PLIP) MPD.8: 4 residues within 4Å: Chain B: Q.35, V.37, T.53, I.63 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.53, B:I.63 Hydrogen bonds: B:Q.35 Water bridges: B:T.53, B:T.53 MPD.9: 6 residues within 4Å: Chain A: G.173 Chain B: G.173 Chain C: G.173, V.175 Ligands: MPD.4, MPD.14 No protein-ligand interaction detected (PLIP) MPD.13: 4 residues within 4Å: Chain C: Q.35, V.37, T.53, I.63 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.53, C:I.63 Hydrogen bonds: C:Q.35 Water bridges: C:T.53, C:T.53 MPD.14: 6 residues within 4Å: Chain A: G.173, V.175 Chain B: G.173 Chain C: G.173 Ligands: MPD.4, MPD.9 No protein-ligand interaction detected (PLIP)

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

CL.5: 8 residues within 4Å: Chain A: Y.137, R.155 Chain B: Y.137, R.155 Chain C: Y.137, R.155 Ligands: CL.10, CL.15 Ligand excluded by PLIP CL.10: 8 residues within 4Å: Chain A: Y.137, R.155 Chain B: Y.137, R.155 Chain C: Y.137, R.155 Ligands: CL.5, CL.15 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain A: Y.137, R.155 Chain B: Y.137, R.155 Chain C: Y.137, R.155 Ligands: CL.5, CL.10 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Linehan, M.P. et al., Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar. J.Biol.Chem. (2021)

Release Date

2021-03-03

Peptides

Putative acetyl transferase protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

C
AAA

Putative acetyl transferase protein