SMTL ID : 6cb2.1

Crystal structure of Escherichia coli UppP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: P.161, K.162, E.163, R.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.162, A:E.163 Salt bridges: A:R.165 SO4.2: 5 residues within 4Å: Chain A: R.165, R.175 Chain B: R.165, R.175 Ligands: SO4.11 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.165, B:R.175, A:R.165, A:R.175 Water bridges: A:M.205 SO4.3: 3 residues within 4Å: Chain A: M.24, H.25, S.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.24, A:S.26, A:S.26, A:S.26 SO4.4: 3 residues within 4Å: Chain A: H.130, K.134, K.234 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.130, A:K.134, A:K.234 SO4.10: 4 residues within 4Å: Chain B: P.161, K.162, E.163, R.165 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.162, B:E.163 Salt bridges: B:R.165 SO4.11: 5 residues within 4Å: Chain A: R.165, R.175 Chain B: R.165, R.175 Ligands: SO4.2 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:M.205 Salt bridges: B:R.165, B:R.175, A:R.165, A:R.175 SO4.12: 3 residues within 4Å: Chain B: M.24, H.25, S.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.26, B:S.26, B:S.26 SO4.13: 3 residues within 4Å: Chain B: H.130, K.134, K.234 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.130, B:K.134, B:K.234

10 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.5: 10 residues within 4Å: Chain A: L.117, I.120, T.173, Y.174, F.178 Chain B: V.148, L.151, A.155, C.158, L.159 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.117, A:Y.174, A:F.178, B:V.148, B:L.151, B:A.155, B:L.159 Hydrogen bonds: A:Y.174 Water bridges: A:R.175 OLC.6: 7 residues within 4Å: Chain A: L.88, I.92, L.112, I.113, L.116, M.119, P.222 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.88, A:I.92, A:L.112, A:I.113, A:P.222 OLC.7: 5 residues within 4Å: Chain A: V.81, V.82, W.85, L.88, F.89 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.81, A:W.85, A:W.85, A:L.88, A:F.89 Hydrogen bonds: A:V.82 Water bridges: A:R.86 OLC.8: 7 residues within 4Å: Chain A: L.39, L.43, L.58, I.272, P.276, F.277, Y.280 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.39, A:L.58, A:Y.280 OLC.9: 17 residues within 4Å: Chain A: T.40, E.41, S.46, S.47, T.48, M.119, A.187, L.188, P.190, G.191, S.193, R.194, S.195, P.222, M.223, G.226, A.227 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.188 Hydrogen bonds: A:T.40, A:S.47, A:T.48, A:R.194, A:S.195 Water bridges: A:E.41, A:S.46, A:R.194, A:R.194 OLC.14: 10 residues within 4Å: Chain A: V.148, L.151, A.155, C.158, L.159 Chain B: L.117, I.120, T.173, Y.174, F.178 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.148, A:L.151, A:A.155, A:L.159, B:L.117, B:Y.174, B:F.178 Hydrogen bonds: B:Y.174 Water bridges: B:R.175 OLC.15: 7 residues within 4Å: Chain B: L.88, I.92, L.112, I.113, L.116, M.119, P.222 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.88, B:I.92, B:L.112, B:I.113, B:P.222 OLC.16: 5 residues within 4Å: Chain B: V.81, V.82, W.85, L.88, F.89 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.81, B:W.85, B:W.85, B:L.88, B:F.89 Hydrogen bonds: B:V.82 Water bridges: B:R.86 OLC.17: 7 residues within 4Å: Chain B: L.39, L.43, L.58, I.272, P.276, F.277, Y.280 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.39, B:L.58, B:Y.280 OLC.18: 17 residues within 4Å: Chain B: T.40, E.41, S.46, S.47, T.48, M.119, A.187, L.188, P.190, G.191, S.193, R.194, S.195, P.222, M.223, G.226, A.227 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.188 Hydrogen bonds: B:T.40, B:S.47, B:T.48, B:T.48, B:R.194, B:S.195 Water bridges: B:E.41, B:S.46, B:R.194, B:R.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Workman, S.D. et al., Crystal structure of an intramembranal phosphatase central to bacterial cell-wall peptidoglycan biosynthesis and lipid recycling. Nat Commun (2018)

Release Date

2018-03-28

Peptides

Undecaprenyl-diphosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Undecaprenyl-diphosphatase