SMTL ID : 4qn9.1

Structure of human NAPE-PLD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.185, H.187, H.253, D.284 Ligands: ZN.2, 3PE.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.185, A:H.187, A:H.253, A:D.284 ZN.2: 6 residues within 4Å: Chain A: D.189, H.190, D.284, H.343 Ligands: ZN.1, 3PE.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.189, A:H.190, A:D.284, A:H.343 ZN.13: 6 residues within 4Å: Chain B: H.185, H.187, H.253, D.284 Ligands: ZN.14, 3PE.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.185, B:H.187, B:H.253, B:D.284 ZN.14: 6 residues within 4Å: Chain B: D.189, H.190, D.284, H.343 Ligands: ZN.13, 3PE.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.189, B:H.190, B:D.284, B:H.343

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.3: 25 residues within 4Å: Chain A: A.154, P.156, M.160, P.162, H.187, Y.188, D.189, H.253, W.254, K.256, R.257, T.258, L.259, D.284, M.317, Q.320, H.321, H.343, L.349 Ligands: ZN.1, ZN.2, DXC.6, DXC.7, DXC.10, DXC.16 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.162, A:Y.188, A:K.256, A:L.259 Hydrogen bonds: A:Y.188, A:D.189, A:Q.320 Salt bridges: A:H.187, A:H.187, A:H.187, A:H.253, A:H.321, A:H.343 3PE.15: 25 residues within 4Å: Chain B: A.154, P.156, M.160, P.162, H.187, Y.188, D.189, H.253, W.254, K.256, R.257, T.258, L.259, D.284, M.317, Q.320, H.321, H.343, L.349 Ligands: DXC.10, DXC.11, DXC.12, ZN.13, ZN.14, DXC.16 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.162, B:Y.188, B:K.256, B:L.259 Hydrogen bonds: B:Y.188, B:D.189, B:Q.320 Salt bridges: B:H.187, B:H.187, B:H.187, B:H.253, B:H.321, B:H.343

11 x DXC: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID(Non-covalent)

DXC.4: 9 residues within 4Å: Chain A: Y.193, W.218, K.221, C.222 Chain B: Y.159, M.160 Ligands: DXC.11, DXC.16, DXC.19 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.159, B:Y.159, A:K.221 DXC.5: 8 residues within 4Å: Chain A: Y.159, M.160 Chain B: Y.193, W.218, K.221, C.222 Ligands: DXC.6, DXC.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.159, A:Y.159 DXC.6: 5 residues within 4Å: Chain A: M.160 Ligands: 3PE.3, DXC.5, DXC.10, DXC.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.221 DXC.7: 5 residues within 4Å: Chain A: T.258, L.259 Ligands: 3PE.3, DXC.11, DXC.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.258 Hydrogen bonds: A:T.258 DXC.10: 11 residues within 4Å: Chain A: Y.159 Chain B: Y.188, W.218, R.257, T.258 Ligands: 3PE.3, DXC.5, DXC.6, DXC.12, 3PE.15, DXC.16 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.258, A:Y.159, A:Y.159 Salt bridges: B:R.257 Hydrogen bonds: A:Y.159 DXC.11: 5 residues within 4Å: Chain B: M.160 Ligands: DXC.4, DXC.7, 3PE.15, DXC.18 No protein-ligand interaction detected (PLIP) DXC.12: 5 residues within 4Å: Chain B: T.258, L.259 Ligands: DXC.6, DXC.10, 3PE.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.258, B:L.259 DXC.16: 9 residues within 4Å: Chain A: Y.188, W.218, R.257 Chain B: Y.159 Ligands: 3PE.3, DXC.4, DXC.7, DXC.10, 3PE.15 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.159 Hydrogen bonds: B:Y.159, B:Y.159, A:Y.188 Water bridges: A:P.156 Salt bridges: A:R.257 DXC.17: 4 residues within 4Å: Chain B: K.256, L.259, M.260 Ligands: DXC.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.260 Salt bridges: B:K.256 DXC.18: 4 residues within 4Å: Chain B: L.259 Ligands: DXC.11, DXC.17, DXC.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.259 DXC.19: 6 residues within 4Å: Chain B: G.161, P.162, K.163, A.348 Ligands: DXC.4, DXC.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.162 Hydrogen bonds: B:K.163, B:A.348

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

SO4.8: 5 residues within 4Å: Chain A: F.165, R.166, R.167 Chain B: T.171, S.173 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.167, B:S.173 Salt bridges: A:R.166, A:R.167 SO4.9: 4 residues within 4Å: Chain A: S.151, S.152 Chain B: S.151, S.152 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.152, A:S.152 Water bridges: A:S.151, A:S.151, A:R.153 SO4.20: 4 residues within 4Å: Chain A: T.171, S.173 Chain B: R.166, R.167 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.171, A:S.173, B:R.167 Water bridges: A:S.173 Salt bridges: B:K.97, B:R.166, B:R.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magotti, P. et al., Structure of human N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: regulation of fatty acid ethanolamide biosynthesis by bile acids. Structure (2015)

Release Date

2015-06-17

Peptides

N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D