SMTL ID : 5f15.1

Crystal Structure of ArnT from Cupriavidus metallidurans bound to Undecaprenyl phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

76 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)(Non-functional Binders)

MPG.1: 3 residues within 4Å: Chain A: W.228, R.232 Ligands: MPG.58 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.228, A:R.232 MPG.2: 8 residues within 4Å: Chain A: V.34, F.37, A.41, L.42, L.143, L.146, A.440 Ligands: MPG.20 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.34, A:V.34, A:F.37, A:A.41, A:L.42, A:L.146, A:A.440 MPG.3: 4 residues within 4Å: Chain A: M.150, P.346, G.347 Ligands: MPG.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.346 MPG.4: 4 residues within 4Å: Chain A: G.32, L.36 Ligands: MPG.6, MPG.65 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.36 MPG.5: 4 residues within 4Å: Chain A: G.301, Q.375, G.378 Ligands: CL.79 No protein-ligand interaction detected (PLIP) MPG.6: 2 residues within 4Å: Chain A: W.33 Ligands: MPG.4 No protein-ligand interaction detected (PLIP) MPG.7: 7 residues within 4Å: Chain A: I.377, A.380, L.421, L.422, A.425, R.428 Ligands: MPG.66 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.377, A:A.380, A:L.421, A:L.422, A:R.428 MPG.8: 7 residues within 4Å: Chain A: G.123, M.126, R.130, A.135, A.138 Ligands: MPG.9, MPG.55 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.126, A:A.138 MPG.9: 2 residues within 4Å: Ligands: MPG.8, MPG.55 No protein-ligand interaction detected (PLIP) MPG.10: 4 residues within 4Å: Chain A: F.46, D.50, W.108 Ligands: MPG.62 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.46, A:F.46, A:D.50, A:W.108, A:W.108 MPG.11: 3 residues within 4Å: Chain A: L.116, L.120, G.123 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.120 MPG.12: 10 residues within 4Å: Chain A: V.220, M.310, R.311, R.322, L.325, I.329, I.332, V.336, I.340 Ligands: MPG.76 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.325, A:I.329, A:I.332, A:V.336, A:I.340 MPG.13: 4 residues within 4Å: Chain A: F.303, L.356, L.359 Ligands: MPG.43 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.356, A:L.359 MPG.14: 2 residues within 4Å: Chain A: A.331, F.335 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.331, A:F.335, A:F.335 MPG.15: 3 residues within 4Å: Chain A: F.251, S.255 Ligands: MPG.48 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.251 MPG.16: 6 residues within 4Å: Chain A: G.283, S.284, Y.287, L.289 Ligands: MPG.72, MPG.73 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.289 MPG.17: 5 residues within 4Å: Chain A: F.174, W.191, A.194, A.198 Ligands: MPG.57 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.194 MPG.18: 2 residues within 4Å: Chain A: A.237 Ligands: MPG.59 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.237 MPG.19: 3 residues within 4Å: Chain A: F.37, V.40 Ligands: MPG.31 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.37, A:V.40 MPG.20: 3 residues within 4Å: Chain A: L.119, M.126 Ligands: MPG.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.119 MPG.21: 6 residues within 4Å: Chain A: G.283, V.285, I.340, R.342, K.344 Ligands: MPG.39 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.340 MPG.22: 2 residues within 4Å: Chain A: W.75 Ligands: MPG.49 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.75 MPG.23: 5 residues within 4Å: Chain A: W.94, V.95, V.98, L.112, L.116 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.94, A:V.95, A:V.98, A:L.112, A:L.116 MPG.24: 1 residues within 4Å: Chain A: I.246 No protein-ligand interaction detected (PLIP) MPG.25: 8 residues within 4Å: Chain A: P.290, L.291, I.293, G.294, L.297 Ligands: MPG.46, MPG.56, MPG.72 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.290, A:L.291, A:I.293, A:L.297 MPG.26: 5 residues within 4Å: Chain A: V.153, Y.409, F.450, H.457 Ligands: MPG.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.153, A:F.450 MPG.27: 4 residues within 4Å: Chain A: Y.409, V.413, F.417 Ligands: MPG.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.409, A:V.413, A:F.417 MPG.28: 2 residues within 4Å: Chain A: L.429, L.430 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.429, A:L.430 MPG.29: 2 residues within 4Å: Chain A: L.430 Ligands: MPG.31 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.430 MPG.30: 2 residues within 4Å: Chain A: W.33, R.433 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.33 MPG.31: 5 residues within 4Å: Chain A: L.422, V.441, M.444 Ligands: MPG.19, MPG.29 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.422, A:V.441 MPG.32: 3 residues within 4Å: Chain A: V.285, F.286, I.340 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.285, A:F.286, A:I.340 MPG.33: 2 residues within 4Å: Chain A: V.44, V.47 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.44, A:V.47 MPG.34: 4 residues within 4Å: Chain A: V.415 Ligands: MPG.35, MPG.60, MPG.61 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.415 MPG.35: 4 residues within 4Å: Chain A: S.390, P.391, A.410 Ligands: MPG.34 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.410 MPG.36: 2 residues within 4Å: Chain A: L.388 Ligands: MPG.37 No protein-ligand interaction detected (PLIP) MPG.37: 2 residues within 4Å: Chain A: L.388 Ligands: MPG.36 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.388 MPG.38: 2 residues within 4Å: Chain A: P.262 Ligands: MPG.48 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.262, A:P.262 MPG.39: 3 residues within 4Å: Chain A: T.275, R.342 Ligands: MPG.21 No protein-ligand interaction detected (PLIP) MPG.40: 3 residues within 4Å: Chain A: L.244, V.245 Ligands: MPG.51 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.244, A:L.244 MPG.41: 7 residues within 4Å: Chain A: W.412, V.452, L.455, G.456, E.458 Ligands: MPG.61, MPG.67 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.412, A:W.412, A:L.455, A:E.458 MPG.42: 2 residues within 4Å: Chain A: R.370, R.428 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.370 MPG.43: 3 residues within 4Å: Chain A: P.304, W.307 Ligands: MPG.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.304, A:W.307 MPG.44: 1 residues within 4Å: Ligands: MPG.45 No protein-ligand interaction detected (PLIP) MPG.45: 4 residues within 4Å: Chain A: W.108 Ligands: MPG.44, MPG.63, EPE.77 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.108 MPG.46: 2 residues within 4Å: Ligands: MPG.25, MPG.47 No protein-ligand interaction detected (PLIP) MPG.47: 3 residues within 4Å: Chain A: L.297 Ligands: MPG.3, MPG.46 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.297 MPG.48: 4 residues within 4Å: Chain A: L.208, F.266 Ligands: MPG.15, MPG.38 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.208, A:F.266 MPG.49: 4 residues within 4Å: Chain A: G.73, W.75 Ligands: MPG.22, MPG.50 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.75, A:W.75, A:W.75 MPG.50: 4 residues within 4Å: Chain A: G.73, W.75, V.76 Ligands: MPG.49 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.75, A:V.76 MPG.51: 3 residues within 4Å: Chain A: Y.252 Ligands: MPG.40, MPG.52 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.252, A:Y.252 MPG.52: 2 residues within 4Å: Chain A: Y.252 Ligands: MPG.51 No protein-ligand interaction detected (PLIP) MPG.53: 2 residues within 4Å: Chain A: L.396 Ligands: MPG.54 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.396 MPG.54: 3 residues within 4Å: Chain A: L.396 Ligands: MPG.53, MPG.75 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.396, A:L.396 MPG.55: 2 residues within 4Å: Ligands: MPG.8, MPG.9 No protein-ligand interaction detected (PLIP) MPG.56: 2 residues within 4Å: Chain A: Y.287 Ligands: MPG.25 No protein-ligand interaction detected (PLIP) MPG.57: 1 residues within 4Å: Ligands: MPG.17 No protein-ligand interaction detected (PLIP) MPG.58: 2 residues within 4Å: Chain A: W.231 Ligands: MPG.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.231, A:W.231 MPG.59: 2 residues within 4Å: Chain A: A.237 Ligands: MPG.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.237 MPG.60: 3 residues within 4Å: Chain A: V.415 Ligands: MPG.34, MPG.67 No protein-ligand interaction detected (PLIP) MPG.61: 4 residues within 4Å: Chain A: W.412, T.459 Ligands: MPG.34, MPG.41 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.412, A:T.459 MPG.62: 1 residues within 4Å: Ligands: MPG.10 No protein-ligand interaction detected (PLIP) MPG.63: 1 residues within 4Å: Ligands: MPG.45 No protein-ligand interaction detected (PLIP) MPG.64: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPG.65: 2 residues within 4Å: Ligands: MPG.4, MPG.68 No protein-ligand interaction detected (PLIP) MPG.66: 3 residues within 4Å: Chain A: R.428, L.429 Ligands: MPG.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.428 MPG.67: 3 residues within 4Å: Chain A: L.455 Ligands: MPG.41, MPG.60 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.455 MPG.68: 1 residues within 4Å: Ligands: MPG.65 No protein-ligand interaction detected (PLIP) MPG.69: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPG.70: 1 residues within 4Å: Chain A: L.223 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.223 MPG.71: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPG.72: 2 residues within 4Å: Ligands: MPG.16, MPG.25 No protein-ligand interaction detected (PLIP) MPG.73: 1 residues within 4Å: Ligands: MPG.16 No protein-ligand interaction detected (PLIP) MPG.74: 1 residues within 4Å: Chain A: R.433 No protein-ligand interaction detected (PLIP) MPG.75: 1 residues within 4Å: Ligands: MPG.54 No protein-ligand interaction detected (PLIP) MPG.76: 2 residues within 4Å: Chain A: V.224 Ligands: MPG.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.224

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.77: 10 residues within 4Å: Chain A: D.50, M.51, R.52, H.53, L.105, G.106, E.107, W.108, Q.109 Ligands: MPG.45 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.53, A:E.107, A:Q.109 Salt bridges: A:D.50, A:D.50, A:E.107, A:E.107

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

PO4.78: 3 residues within 4Å: Chain A: H.235, L.236, A.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.235, A:L.236, A:A.237

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

CL.79: 3 residues within 4Å: Chain A: K.305, K.374 Ligands: MPG.5 Ligand excluded by PLIP CL.80: 4 residues within 4Å: Chain A: R.52, V.55, H.457, E.458 Ligand excluded by PLIP

1 x 5TR: [(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate(Non-covalent)

5TR.81: 23 residues within 4Å: Chain A: K.88, L.172, M.175, W.196, M.199, K.206, I.211, A.212, P.214, G.215, L.216, L.218, H.270, W.271, R.273, Y.274, T.275, M.326, W.330, F.337, S.341, L.345, Y.348 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.172, A:M.175, A:W.196, A:W.196, A:I.211, A:A.212, A:P.214, A:L.216, A:L.218, A:L.218, A:W.271, A:R.273, A:Y.274, A:Y.274, A:Y.274, A:Y.274, A:T.275, A:W.330, A:F.337, A:Y.348 Water bridges: A:K.88 Salt bridges: A:K.88, A:R.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrou, V.I. et al., Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation. Science (2016)

Release Date

2016-02-17

Peptides

4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase

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