SMTL ID : 4o6m.1

Structure of AF2299, a CDP-alcohol phosphotransferase (CMP-bound)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: T.206, D.242, D.245, D.263 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.242, A:D.242, A:D.263, H2O.3, H2O.4 CA.14: 5 residues within 4Å: Chain B: D.242, D.245, G.246, D.263 Ligands: C5P.35 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.245, B:D.245, B:D.263, B:D.263, H2O.7

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

MPG.2: 5 residues within 4Å: Chain A: Q.204, V.207, F.208 Ligands: MPG.4, MPG.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.207, A:V.207 MPG.3: 7 residues within 4Å: Chain A: I.191, L.195, V.200, Q.204, I.205, F.208, I.241 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.195, A:Q.204, A:F.208, A:F.208 MPG.4: 8 residues within 4Å: Chain A: N.203, V.207, F.210, Y.258, L.262, L.266 Chain B: I.364 Ligands: MPG.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.207 MPG.5: 2 residues within 4Å: Chain A: V.207 Ligands: MPG.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.207 MPG.6: 1 residues within 4Å: Chain A: F.208 No protein-ligand interaction detected (PLIP) MPG.7: 7 residues within 4Å: Chain A: I.292, L.295, V.350, A.353, L.354, N.357, F.358 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.295, A:A.353, A:N.357, A:F.358 MPG.8: 3 residues within 4Å: Chain A: A.218, L.221, L.222 No protein-ligand interaction detected (PLIP) MPG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPG.15: 4 residues within 4Å: Chain B: L.195, T.198, V.200 Ligands: MPG.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.200 MPG.16: 9 residues within 4Å: Chain B: I.191, L.195, V.200, Q.204, I.205, F.208, I.241 Ligands: MPG.15, MPG.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.204, B:F.208, B:F.208 MPG.17: 5 residues within 4Å: Chain B: I.191, L.194, L.195, T.198 Ligands: MPG.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.191, B:T.198 MPG.18: 5 residues within 4Å: Chain B: I.292, L.295, V.350, A.353, L.354 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.353, B:L.354, B:L.354 MPG.19: 4 residues within 4Å: Chain B: L.347, V.350, I.351, L.354 No protein-ligand interaction detected (PLIP) MPG.20: 8 residues within 4Å: Chain A: I.364 Chain B: N.203, V.207, Y.258, L.262, L.266 Ligands: MPG.25, MPG.26 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.207, B:Y.258, A:I.364 MPG.21: 6 residues within 4Å: Chain B: I.335, A.338, C.339, V.342, L.347, I.351 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.338, B:L.347 MPG.22: 1 residues within 4Å: Ligands: MPG.29 No protein-ligand interaction detected (PLIP) MPG.23: 2 residues within 4Å: Chain B: W.178 Ligands: MPG.30 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.178 MPG.24: 10 residues within 4Å: Chain B: F.211, L.214, V.215, S.217, A.218, L.221, I.273, S.277 Ligands: MPG.25, MPG.26 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.218 MPG.25: 6 residues within 4Å: Chain B: F.210, L.214, Y.269, I.273 Ligands: MPG.20, MPG.24 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.210, B:F.210, B:Y.269 MPG.26: 6 residues within 4Å: Chain B: V.207, F.210, F.211, L.214 Ligands: MPG.20, MPG.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.210 MPG.27: 4 residues within 4Å: Chain B: A.218, L.221, L.222 Ligands: MPG.28 No protein-ligand interaction detected (PLIP) MPG.28: 3 residues within 4Å: Chain B: L.221, Y.280 Ligands: MPG.27 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.221, B:Y.280 MPG.29: 1 residues within 4Å: Ligands: MPG.22 No protein-ligand interaction detected (PLIP) MPG.30: 4 residues within 4Å: Chain B: W.178, P.326, F.331 Ligands: MPG.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.178, B:F.331

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain A: T.201, N.203, Q.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.201, A:N.203 SO4.11: 7 residues within 4Å: Chain A: D.176, R.268, I.303, A.304, T.328, R.329, R.332 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.329 Water bridges: A:R.268, A:I.303 Salt bridges: A:R.268, A:R.332 SO4.12: 3 residues within 4Å: Chain A: G.96, R.97, G.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97 Salt bridges: A:R.97 SO4.13: 5 residues within 4Å: Chain A: P.320, E.321, G.322, R.362, A.366 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.321 Water bridges: A:G.322 Salt bridges: A:R.362 SO4.31: 3 residues within 4Å: Chain B: G.96, R.97, G.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.97 SO4.32: 7 residues within 4Å: Chain B: Y.174, R.268, I.303, A.304, T.328, R.329, R.332 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.174, B:I.303, B:R.329 Water bridges: B:R.268 Salt bridges: B:R.268, B:R.332 SO4.33: 1 residues within 4Å: Chain B: Q.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.204 SO4.34: 4 residues within 4Å: Chain B: S.224, Y.225, L.226, N.343 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.225, B:L.226

1 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.35: 18 residues within 4Å: Chain B: K.164, R.185, P.202, N.203, T.206, D.242, G.243, D.245, G.246, E.247, A.249, R.250, E.255, S.256, G.259, A.260, D.263 Ligands: CA.14 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.245, B:D.263 Hydrogen bonds: B:T.206, B:G.243, B:G.246, B:R.250, B:S.256 Water bridges: B:S.256, B:S.256, A:K.309 Salt bridges: B:K.164, B:R.185, B:R.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sciara, G. et al., Structural basis for catalysis in a CDP-alcohol phosphotransferase. Nat Commun (2014)

Release Date

2014-05-14

Peptides

AF2299, a CDP-alcohol phosphotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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AF2299, a CDP-alcohol phosphotransferase

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