SMTL ID : 5ezm.1

Crystal Structure of ArnT from Cupriavidus metallidurans in the apo state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.87, H.268, H.270 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.87, A:E.87, A:H.268, A:H.270

1 x DSL: MONO-TRANS, OCTA-CIS DECAPRENYL-PHOSPHATE(Non-covalent)

DSL.2: 13 residues within 4Å: Chain A: V.171, L.172, M.175, C.195, W.196, M.199, I.211, P.214, G.215, V.217, L.218, M.326, W.330 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.171, A:M.175, A:W.196, A:W.196, A:I.211, A:P.214, A:V.217, A:L.218, A:W.330, A:W.330

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

MPG.3: 5 residues within 4Å: Chain A: F.303, L.306, I.332, L.359 Ligands: MPG.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.303, A:L.306, A:I.332, A:L.359 MPG.4: 4 residues within 4Å: Chain A: F.303, F.335 Ligands: MPG.3, MPG.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.303, A:F.303, A:F.335 MPG.5: 7 residues within 4Å: Chain A: L.116, L.119, L.120, G.123, V.124 Ligands: MPG.9, MPG.35 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.120 MPG.6: 3 residues within 4Å: Chain A: W.33 Ligands: MPG.24, MPG.40 No protein-ligand interaction detected (PLIP) MPG.7: 5 residues within 4Å: Chain A: V.95, V.98, G.99, L.112, L.116 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.95, A:V.98, A:L.112, A:L.116 MPG.8: 5 residues within 4Å: Chain A: K.374, Q.375, G.378, M.379 Ligands: MPG.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.374 MPG.9: 5 residues within 4Å: Chain A: G.123, M.126, A.135, A.138 Ligands: MPG.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.135, A:A.138 MPG.10: 3 residues within 4Å: Chain A: T.247, F.251, S.255 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.251 MPG.11: 7 residues within 4Å: Chain A: M.150, A.154, G.294, L.297, G.347 Ligands: MPG.12, MPG.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.154, A:L.297 MPG.12: 2 residues within 4Å: Chain A: P.346 Ligands: MPG.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.346 MPG.13: 7 residues within 4Å: Chain A: V.153, F.157, F.450, L.454, H.457 Ligands: MPG.11, MPG.47 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.153, A:F.157, A:F.450, A:L.454 MPG.14: 5 residues within 4Å: Chain A: A.300, G.301, P.304 Ligands: MPG.4, MPG.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.304 MPG.15: 5 residues within 4Å: Chain A: W.75, V.76, W.94, I.246 Ligands: MPG.44 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.75, A:V.76, A:W.94, A:W.94 MPG.16: 3 residues within 4Å: Chain A: Y.287, P.290, G.294 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.287, A:P.290 MPG.17: 1 residues within 4Å: Chain A: F.46 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.46 MPG.18: 6 residues within 4Å: Chain A: L.120, A.187, W.191, A.194, A.198, V.201 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.120, A:W.191, A:A.194, A:V.201 MPG.19: 1 residues within 4Å: Chain A: F.266 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.266, A:F.266 MPG.20: 1 residues within 4Å: Chain A: A.39 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.39 MPG.21: 2 residues within 4Å: Chain A: V.40, V.43 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.43 MPG.22: 4 residues within 4Å: Chain A: V.47, M.51, V.452, L.455 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.47, A:V.452, A:L.455 MPG.23: 4 residues within 4Å: Chain A: W.412, L.455, T.459 Ligands: MPG.32 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.412, A:W.412, A:L.455, A:T.459 MPG.24: 3 residues within 4Å: Chain A: F.37 Ligands: MPG.6, MPG.31 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.37 MPG.25: 5 residues within 4Å: Chain A: V.220, W.307, M.310, R.311, V.336 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.220, A:W.307, A:R.311, A:V.336 MPG.26: 2 residues within 4Å: Chain A: I.377, R.428 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.377, A:R.428 MPG.27: 2 residues within 4Å: Chain A: G.32, W.33 No protein-ligand interaction detected (PLIP) MPG.28: 5 residues within 4Å: Chain A: V.34, L.143, L.146, P.437, A.440 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.34, A:L.146, A:P.437, A:A.440 MPG.29: 1 residues within 4Å: Chain A: R.131 No protein-ligand interaction detected (PLIP) MPG.30: 2 residues within 4Å: Chain A: W.307, T.308 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.307, A:T.308 MPG.31: 1 residues within 4Å: Ligands: MPG.24 No protein-ligand interaction detected (PLIP) MPG.32: 1 residues within 4Å: Ligands: MPG.23 No protein-ligand interaction detected (PLIP) MPG.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPG.34: 1 residues within 4Å: Chain A: L.119 No protein-ligand interaction detected (PLIP) MPG.35: 2 residues within 4Å: Ligands: MPG.5, MPG.38 No protein-ligand interaction detected (PLIP) MPG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPG.37: 3 residues within 4Å: Chain A: F.337 Ligands: MPG.45, MPG.49 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.337 MPG.38: 3 residues within 4Å: Chain A: L.120, F.174 Ligands: MPG.35 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.120, A:F.174 MPG.39: 1 residues within 4Å: Chain A: L.430 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.430 MPG.40: 2 residues within 4Å: Chain A: W.33 Ligands: MPG.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.33, A:W.33 MPG.41: 3 residues within 4Å: Chain A: F.46, D.50, W.108 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.46, A:F.46, A:F.46, A:D.50, A:W.108, A:W.108 MPG.42: 3 residues within 4Å: Chain A: S.284, F.286, Y.287 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.286, A:Y.287 MPG.43: 4 residues within 4Å: Chain A: F.70, W.75, V.98, E.101 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.75, A:W.75, A:V.98, A:E.101 MPG.44: 3 residues within 4Å: Chain A: G.73, W.75 Ligands: MPG.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.75 MPG.45: 9 residues within 4Å: Chain A: K.206, V.209, A.212, F.337, F.338, Y.348 Ligands: MPG.37, MPG.49, PC.55 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.206, A:V.209, A:A.212, A:F.337, A:Y.348 MPG.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPG.47: 3 residues within 4Å: Chain A: V.413, A.453 Ligands: MPG.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.413, A:A.453 MPG.48: 2 residues within 4Å: Chain A: F.266 Ligands: MPG.49 No protein-ligand interaction detected (PLIP) MPG.49: 8 residues within 4Å: Chain A: I.340, S.341, R.342 Ligands: MPG.37, MPG.45, MPG.48, MPG.50, PC.55 No protein-ligand interaction detected (PLIP) MPG.50: 4 residues within 4Å: Chain A: E.269, H.270 Ligands: MPG.49, PC.55 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.269, A:H.270

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

CL.51: 2 residues within 4Å: Chain A: R.67, L.105 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain A: R.462, D.468 Ligand excluded by PLIP

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

PO4.53: 4 residues within 4Å: Chain A: R.232, H.235, L.236, A.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.236, A:A.237 Water bridges: A:L.238 PO4.54: 2 residues within 4Å: Chain A: L.223, V.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.224

1 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.55: 9 residues within 4Å: Chain A: E.87, G.207, L.208, F.265, F.266, H.268 Ligands: MPG.45, MPG.49, MPG.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.208

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

EPE.56: 7 residues within 4Å: Chain A: D.50, H.53, L.105, G.106, E.107, W.108, Q.109 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.50, A:D.50, A:E.107, A:Q.109 Salt bridges: A:D.50, A:D.50, A:E.107, A:E.107

Links

RCSB   PDBe   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 transferase or related glycosyltransferases of PMT family: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

4-amino-4-deoxy-L-arabinose transferase or related glycosyltransferases of PMT family

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