SMTL ID : 6h7f.1

Crystal structure of BauA, the Ferric preacinetobactin receptor from Acinetobacter baumannii in complex with Fe3+-Preacinetobactin-acinetobactin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-trimer

Ligands

3 x FE: FE (III) ION(Non-functional Binders)

FE.1: 3 residues within 4Å: Ligands: FV8.2, OPV.3, OPZ.4 No protein-ligand interaction detected (PLIP) FE.24: 2 residues within 4Å: Ligands: FV8.25, OPZ.26 No protein-ligand interaction detected (PLIP) FE.52: 2 residues within 4Å: Ligands: FV8.53, OPZ.54 No protein-ligand interaction detected (PLIP)

3 x FV8: (4~{S},5~{R})-2-[2,3-bis(oxidanyl)phenyl]-~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-~{N}-oxidanyl-4,5-dihydro-1,3-oxazole-4-carboxamide(Non-covalent)

FV8.2: 20 residues within 4Å: Chain A: W.100, Y.128, R.256, Y.315, Y.317, A.320, S.321, G.337, Q.338, L.339, F.341, G.380, Y.381, R.382, L.413, L.687 Ligands: FE.1, OPV.3, OPZ.4, EDO.23 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.100, A:Y.317, A:R.382, A:L.413 Hydrogen bonds: A:R.256, A:R.256, A:Y.315 Water bridges: A:D.378, A:D.378, A:D.378 FV8.25: 17 residues within 4Å: Chain B: W.100, Y.128, R.256, Y.315, Y.317, A.320, S.321, Q.338, L.339, G.380, Y.381, R.382, L.413, L.687 Ligands: FE.24, OPZ.26, EDO.51 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.100, B:Y.317, B:L.339, B:L.413 Hydrogen bonds: B:R.256, B:R.256 Water bridges: B:D.378, B:D.378 FV8.53: 16 residues within 4Å: Chain C: W.100, Y.128, R.256, Y.315, Y.317, G.337, Q.338, L.339, G.380, Y.381, R.382, L.413, L.687 Ligands: FE.52, OPZ.54, EDO.81 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.100, C:Y.317, C:L.413 Hydrogen bonds: C:R.256, C:R.256, C:Y.315, C:R.382 Water bridges: C:D.378, C:D.378, C:D.378

1 x OPV: ~{N}-[(4~{S},5~{S})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide(Non-covalent)

OPV.3: 6 residues within 4Å: Chain A: R.256, L.687 Ligands: FE.1, FV8.2, OPZ.4, EDO.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.687 Hydrogen bonds: A:R.256

3 x OPZ: ~{N}-[(4~{S},5~{R})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide(Non-covalent)

OPZ.4: 6 residues within 4Å: Chain A: R.256, L.687 Ligands: FE.1, FV8.2, OPV.3, EDO.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.687 Hydrogen bonds: A:R.256 OPZ.26: 5 residues within 4Å: Chain B: R.256, L.687 Ligands: FE.24, FV8.25, EDO.51 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.687 Hydrogen bonds: B:R.256 OPZ.54: 5 residues within 4Å: Chain C: R.256, L.687 Ligands: FE.52, FV8.53, EDO.81 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.687 Hydrogen bonds: C:R.256

28 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.5: 8 residues within 4Å: Chain A: F.227, Y.245, D.246, K.288, G.289, A.290, Q.310, T.312 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.227, A:D.246, A:A.290 Hydrogen bonds: A:Q.310 C8E.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) C8E.7: 5 residues within 4Å: Chain A: N.607, Q.608, A.609, V.633 Ligands: C8E.31 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.607, A:A.609 C8E.8: 4 residues within 4Å: Chain A: A.482, N.483, Q.513, E.514 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.482 C8E.9: 4 residues within 4Å: Chain A: G.628, N.629, V.654 Chain B: L.700 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.654 C8E.10: 2 residues within 4Å: Chain A: P.466, K.509 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.466 C8E.27: 2 residues within 4Å: Chain B: G.441, P.466 No protein-ligand interaction detected (PLIP) C8E.28: 10 residues within 4Å: Chain B: I.563, F.581, T.582, N.607, A.632, V.633, S.634, K.635, G.648 Ligands: C8E.38 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.563, B:F.581, B:N.607 Hydrogen bonds: B:K.635, B:G.648 C8E.29: 4 residues within 4Å: Chain B: L.302, F.356, W.365, D.427 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.356, B:W.365, B:W.365, B:W.365, B:W.365, B:D.427 C8E.30: 9 residues within 4Å: Chain B: V.468, L.470, A.482, N.483, Q.513, A.530, F.531, I.563, Y.583 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.563, B:Y.583 Hydrogen bonds: B:Q.513 C8E.31: 2 residues within 4Å: Chain B: F.186 Ligands: C8E.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.186 C8E.32: 7 residues within 4Å: Chain B: G.188, V.190, G.208, M.209, R.225, F.227, D.246 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.227 C8E.33: 4 residues within 4Å: Chain B: S.627, G.628 Ligands: C8E.36, C8E.63 No protein-ligand interaction detected (PLIP) C8E.34: 4 residues within 4Å: Chain B: F.298, L.302, F.352, W.365 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.298, B:L.302 C8E.35: 6 residues within 4Å: Chain B: Y.305, A.350, F.352, A.367, N.368, F.423 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.367, B:F.423 C8E.36: 8 residues within 4Å: Chain B: A.613, G.628, N.629, I.630, V.654, L.676 Chain C: L.700 Ligands: C8E.33 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.700, B:V.654, B:L.676 C8E.37: 5 residues within 4Å: Chain B: F.227, A.244, Y.245, D.246, K.288 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.227, B:F.227, B:A.244, B:K.288 C8E.38: 3 residues within 4Å: Chain B: A.609 Chain C: F.186 Ligands: C8E.28 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.609, C:F.186, C:F.186 C8E.55: 5 residues within 4Å: Chain C: Q.513, E.514, L.515, F.531, I.563 No protein-ligand interaction detected (PLIP) C8E.56: 6 residues within 4Å: Chain C: V.468, L.470, A.482, N.483, Y.484, Q.513 No protein-ligand interaction detected (PLIP) C8E.57: 9 residues within 4Å: Chain C: G.188, H.189, V.190, G.208, M.209, R.225, L.226, F.227, D.246 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.190 C8E.58: 11 residues within 4Å: Chain C: G.294, E.295, Y.296, A.304, Y.305, A.306, A.350, G.351, F.352, N.368, F.423 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.423 C8E.59: 10 residues within 4Å: Chain A: A.184, F.186, D.212 Chain C: F.581, T.582, Y.583, N.607, Q.608, V.633, S.634 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.581, C:Y.583, C:Y.583 Water bridges: C:V.633 Hydrogen bonds: A:D.212 C8E.60: 5 residues within 4Å: Chain C: L.611, G.628, N.629, V.654 Ligands: C8E.62 No protein-ligand interaction detected (PLIP) C8E.61: 5 residues within 4Å: Chain C: K.316, D.342, Y.379, T.409, P.410 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.342 C8E.62: 8 residues within 4Å: Chain A: L.676, R.696 Chain B: L.676, R.696, Y.698 Chain C: R.696, Y.698 Ligands: C8E.60 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.676 Hydrogen bonds: B:Y.698 C8E.63: 5 residues within 4Å: Chain C: A.656, Y.658, A.671, V.702 Ligands: C8E.33 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.656, C:Y.658, C:A.671, C:V.702 C8E.64: 1 residues within 4Å: Chain C: I.478 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.478

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

EDO.11: 6 residues within 4Å: Chain A: L.121, F.122, S.347, A.348, Y.371, Y.372 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: V.260, T.262, N.639, L.644, N.689 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: T.643, L.644, S.645 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: N.218, T.274, L.275, D.397, P.398, P.400 Chain C: K.268 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: S.537, G.556, E.557, Q.558, L.588, K.590, T.591 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain A: F.423 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: H.250, S.282, V.283, E.284, K.316, N.318, F.408 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: L.470, I.472, V.480, Y.481, A.482 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: Q.42, Y.71, R.576, M.578, G.612, A.613, E.614 Ligands: EDO.22 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain A: V.43, A.44, T.45, S.46, S.47, F.57, T.64, I.65, S.66 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: S.299, D.300, M.303, K.353, G.354, K.355 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain A: A.39, G.40, G.41, Q.42, V.43, G.569, L.577, M.578 Ligands: EDO.19 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: R.382 Ligands: FV8.2, OPV.3, OPZ.4 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: L.121, F.122, S.347, A.348, T.370, Y.371, Y.372 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain B: S.537, G.556, E.557, Q.558, L.588, K.590, T.591 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain B: N.459, K.461, G.502, E.503, I.504 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: V.264, I.266, P.267, S.328 Chain C: N.399 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain B: E.82, Y.674, T.697, M.699 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain B: Y.484, K.511, Q.513, E.532, T.534 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain B: H.250, S.282, V.283, E.284, K.316, N.318 Ligand excluded by PLIP EDO.46: 8 residues within 4Å: Chain B: V.43, A.44, T.45, S.46, F.57, T.64, I.65, S.66 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain A: K.268 Chain B: N.218, T.274, L.275, D.397, P.398, P.400 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain B: S.419, T.420, S.421, T.446, A.460 Ligand excluded by PLIP EDO.49: 1 residues within 4Å: Chain B: T.178 Ligand excluded by PLIP EDO.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain B: R.382 Ligands: FV8.25, OPZ.26 Ligand excluded by PLIP EDO.65: 9 residues within 4Å: Chain C: V.43, A.44, T.45, S.46, S.47, F.57, T.64, I.65, S.66 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain C: H.250, S.282, V.283, E.284, K.316, N.318 Ligand excluded by PLIP EDO.67: 2 residues within 4Å: Chain C: Q.310, T.312 Ligand excluded by PLIP EDO.68: 3 residues within 4Å: Chain C: T.643, L.644, S.645 Ligand excluded by PLIP EDO.69: 5 residues within 4Å: Chain C: N.459, K.461, G.502, E.503, I.504 Ligand excluded by PLIP EDO.70: 8 residues within 4Å: Chain B: K.268 Chain C: N.218, D.273, T.274, L.275, D.397, P.398, P.400 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain C: S.419, T.420, S.421, T.446, K.448 Ligand excluded by PLIP EDO.72: 7 residues within 4Å: Chain C: Q.42, Y.71, R.576, M.578, G.612, E.614 Ligands: EDO.74 Ligand excluded by PLIP EDO.73: 5 residues within 4Å: Chain C: Y.484, K.511, Q.513, E.532, T.534 Ligand excluded by PLIP EDO.74: 11 residues within 4Å: Chain C: Y.38, A.39, G.40, G.41, Q.42, V.43, G.569, R.576, L.577, M.578 Ligands: EDO.72 Ligand excluded by PLIP EDO.75: 6 residues within 4Å: Chain C: N.119, G.120, R.293, Y.305, A.307, D.349 Ligand excluded by PLIP EDO.76: 4 residues within 4Å: Chain C: V.260, N.639, L.644, N.689 Ligand excluded by PLIP EDO.77: 7 residues within 4Å: Chain C: S.537, G.556, E.557, Q.558, L.588, K.590, T.591 Ligand excluded by PLIP EDO.78: 6 residues within 4Å: Chain C: L.121, F.122, S.347, A.348, Y.371, Y.372 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain C: P.270, K.271, T.274, Y.396 Ligand excluded by PLIP EDO.80: 4 residues within 4Å: Chain C: E.82, Y.674, A.694, M.699 Ligand excluded by PLIP EDO.81: 3 residues within 4Å: Chain C: R.382 Ligands: FV8.53, OPZ.54 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moynie, L. et al., Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogenAcinetobacter baumannii. Elife (2018)

Release Date

2018-10-10

Peptides

BauA: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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BauA

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