SMTL ID : 8p90.1

TARGET COMPLEX 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.185, H.187, H.190, 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.12: 7 residues within 4Å: Chain B: H.185, H.187, H.190, H.253, D.284 Ligands: ZN.13, 3PE.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.185, B:H.187, B:H.253, B:D.284 ZN.13: 8 residues within 4Å: Chain B: H.132, D.189, H.190, D.284, H.321, H.343 Ligands: ZN.12, 3PE.14 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: 26 residues within 4Å: Chain A: R.82, 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.5, DXC.7, DXC.8, DXC.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.82, A:P.156, A:P.162, A:Y.188, A:L.259 Hydrogen bonds: A:Y.188 Salt bridges: A:H.187, A:H.187, A:H.187, A:H.253, A:H.321, A:H.343 3PE.14: 25 residues within 4Å: Chain B: W.83, A.154, P.156, M.160, P.162, H.187, Y.188, D.189, H.253, W.254, K.256, R.257, L.259, D.284, M.317, Q.320, H.321, H.343, L.349 Ligands: DXC.7, DXC.10, DXC.11, ZN.12, ZN.13, DXC.17 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.83, B:P.162, B:Y.188, B:L.259 Hydrogen bonds: B:W.83, 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

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

DXC.4: 8 residues within 4Å: Chain A: Y.193, W.218, K.221, C.222 Chain B: Y.159, M.160 Ligands: DXC.7, DXC.16 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.159, B:Y.159, A:W.218, A:W.218, A:K.221 DXC.5: 5 residues within 4Å: Chain A: L.84 Ligands: 3PE.3, DXC.8, DXC.11, DXC.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.84 DXC.6: 4 residues within 4Å: Chain A: T.258, L.259, M.260 Ligands: DXC.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.258 DXC.7: 8 residues within 4Å: Chain A: Y.188, W.218, R.257 Chain B: Y.159 Ligands: 3PE.3, DXC.4, DXC.10, 3PE.14 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.159, B:Y.159, B:Y.159 Hydrogen bonds: B:Y.159, A:Y.188 Salt bridges: A:R.257 DXC.8: 6 residues within 4Å: Chain A: L.81, R.82, L.84, I.85 Ligands: 3PE.3, DXC.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.81, A:R.82, A:L.84, A:I.85 DXC.10: 13 residues within 4Å: Chain A: P.156, S.157, Y.159, M.160 Chain B: Y.188, W.218, R.257, T.258 Ligands: 3PE.3, DXC.7, DXC.11, 3PE.14, DXC.15 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.159, A:Y.159, A:Y.159, B:T.258 Hydrogen bonds: A:P.156 Salt bridges: B:R.257 DXC.11: 5 residues within 4Å: Chain B: T.258, L.259 Ligands: DXC.5, DXC.10, 3PE.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.258, B:T.258, B:L.259 DXC.15: 8 residues within 4Å: Chain A: Y.159, M.160 Chain B: Y.193, W.218, K.221, C.222 Ligands: DXC.5, DXC.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.159, A:Y.159 DXC.16: 4 residues within 4Å: Chain B: M.160 Ligands: DXC.4, DXC.6, DXC.17 No protein-ligand interaction detected (PLIP) DXC.17: 5 residues within 4Å: Chain B: R.82, L.84, L.259 Ligands: 3PE.14, DXC.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.82, B:L.84, B:L.259

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.9: 8 residues within 4Å: Chain A: S.151, S.152, K.163, N.194 Chain B: F.150, S.151, S.152, N.194 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.151, A:S.152, A:S.152, A:Q.158, B:N.194 Salt bridges: A:K.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garau, G., TARGET COMPLEX 2. To Be Published

Release Date

2024-06-26

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

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