SMTL ID : 5kf9.1

X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum in complex with N-acetylglucosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 13 residues within 4Å: Chain A: R.192, W.193, E.196, P.235, G.251, P.252, I.253, I.286, D.287, W.288, T.289, Y.297 Ligands: EP1.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.286, A:T.289 Hydrogen bonds: A:R.192, A:I.253, A:D.287, A:D.287, A:D.287, A:W.288 Water bridges: A:R.192, A:Y.297 NAG.8: 13 residues within 4Å: Chain B: R.192, W.193, E.196, P.235, G.251, P.252, I.253, I.286, D.287, W.288, T.289, Y.297 Ligands: EP1.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.286, B:T.289 Hydrogen bonds: B:R.192, B:I.253, B:D.287, B:D.287, B:D.287, B:W.288 Water bridges: B:R.192

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

ACO.2: 23 residues within 4Å: Chain A: I.78, S.80, I.81, I.82, V.83, R.88, H.89, Q.90, G.91, I.92, G.93, T.94, C.114, G.115, P.126, C.129, P.131, S.132, E.134, F.135, V.138 Chain B: N.295 Ligands: EDO.5 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.83, A:F.135 Hydrogen bonds: A:I.81, A:I.81, A:V.83, A:R.88, A:H.89, A:Q.90, A:G.91, A:I.92, A:G.93, A:T.94, A:T.94, A:T.94, A:S.132, B:N.295, B:N.295 Water bridges: A:F.87, A:S.132 Salt bridges: A:H.89 pi-Cation interactions: A:H.89 ACO.9: 23 residues within 4Å: Chain A: N.295 Chain B: I.78, S.80, I.81, I.82, V.83, R.88, H.89, Q.90, G.91, I.92, G.93, T.94, C.114, G.115, P.126, C.129, P.131, S.132, E.134, F.135, V.138 Ligands: EDO.12 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.83, B:F.135 Hydrogen bonds: B:I.81, B:I.81, B:V.83, B:H.89, B:Q.90, B:G.91, B:I.92, B:G.93, B:T.94, B:T.94, B:S.132, A:N.295, A:N.295 Water bridges: B:F.87, B:R.88, B:S.132 Salt bridges: B:H.89 pi-Cation interactions: B:H.89

2 x COA: COENZYME A(Non-covalent)

COA.3: 12 residues within 4Å: Chain A: F.189, W.193, G.254, I.255, R.260, K.261, Q.262, G.263, L.264, G.265, R.266 Ligands: EP1.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.189, A:W.193, A:I.255 Hydrogen bonds: A:I.255, A:K.261, A:G.263, A:G.263, A:L.264, A:G.265, A:R.266 Water bridges: A:K.261, A:Q.262 COA.10: 12 residues within 4Å: Chain B: F.189, W.193, G.254, I.255, R.260, K.261, Q.262, G.263, L.264, G.265, R.266 Ligands: EP1.14 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.189, B:W.193, B:I.255 Hydrogen bonds: B:I.255, B:K.261, B:G.263, B:G.263, B:L.264, B:G.265, B:R.266 Water bridges: B:K.261, B:Q.262

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

EDO.4: 6 residues within 4Å: Chain A: R.41, K.42, K.43, Y.59, E.103, L.104 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.42, A:K.42 EDO.5: 8 residues within 4Å: Chain A: N.19, I.85, R.88 Chain B: G.298, N.301, F.302, M.303 Ligands: ACO.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.19, A:R.88, A:R.88, B:G.298 EDO.6: 6 residues within 4Å: Chain A: I.151, L.242, K.283, W.305 Chain B: T.22, V.23 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.242, A:K.283, B:T.22 EDO.11: 6 residues within 4Å: Chain B: R.41, K.42, K.43, Y.59, E.103, L.104 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.42, B:K.42 EDO.12: 8 residues within 4Å: Chain A: G.298, N.301, F.302, M.303 Chain B: N.19, I.85, R.88 Ligands: ACO.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.19, B:R.88, B:R.88, A:G.298 EDO.13: 6 residues within 4Å: Chain A: T.22, V.23 Chain B: I.151, L.242, K.283, W.305 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.22, B:L.242, B:K.283

2 x EP1: 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID(Non-covalent)

EP1.7: 11 residues within 4Å: Chain A: F.147, F.189, S.190, G.191, R.192, W.193, W.288, T.289, E.290 Ligands: NAG.1, COA.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.191, A:R.192, A:W.193, A:E.290 Water bridges: A:E.290, A:E.290 EP1.14: 11 residues within 4Å: Chain B: F.147, F.189, S.190, G.191, R.192, W.193, W.288, T.289, E.290 Ligands: NAG.8, COA.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.191, B:R.192, B:W.193, B:E.290 Water bridges: B:E.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dopkins, B.J. et al., Structural Studies on a Glucosamine/Glucosaminide N-Acetyltransferase. Biochemistry (2016)

Release Date

2016-07-06

Peptides

Predicted acetyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Predicted acetyltransferase

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