SMTL ID : 8pc4.1

MEMBRANE TARGET COMPLEX 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: H.185, H.187, D.189, 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: 7 residues within 4Å: Chain B: H.132, D.189, H.190, D.284, 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: 25 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.6, DXC.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.162, A:Y.188, A:L.259 Hydrogen bonds: A:Y.188, A:Q.320 Salt bridges: A:H.187, A:H.187, A:H.187, A:H.253, A:H.321, A:H.343 3PE.14: 26 residues within 4Å: Chain B: W.83, A.154, S.155, 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, Q.320, H.321, H.343, L.349 Ligands: DXC.7, DXC.11, ZN.12, ZN.13, DXC.15, DXC.16 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.83, B:P.156, B:P.162, B:Y.188, B:Y.188, B:K.256, B:T.258, B:L.259 Hydrogen bonds: B:Y.188, 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: 9 residues within 4Å: Chain A: Y.193, W.218, K.221, C.222 Chain B: I.85, Y.159, M.160 Ligands: DXC.7, DXC.15 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.159, B:Y.159, A:W.218, A:W.218 DXC.5: 5 residues within 4Å: Chain A: M.160 Ligands: 3PE.3, DXC.8, DXC.9, DXC.11 No protein-ligand interaction detected (PLIP) DXC.6: 5 residues within 4Å: Chain A: T.258, L.259 Ligands: 3PE.3, DXC.7, DXC.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.259 Hydrogen bonds: A:L.259, A:L.259 DXC.7: 9 residues within 4Å: Chain A: Y.188, W.218, R.257, T.258 Chain B: Y.159 Ligands: DXC.4, DXC.6, DXC.10, 3PE.14 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.159, B:Y.159, A:T.258 Hydrogen bonds: B:Y.159 Salt bridges: A:R.257 DXC.8: 9 residues within 4Å: Chain A: K.88, Y.159, M.160 Chain B: Y.193, W.218, K.221, C.222 Ligands: DXC.5, DXC.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.159, A:Y.159, B:K.221 Salt bridges: A:K.88 DXC.9: 5 residues within 4Å: Chain A: L.81, R.82, L.84, I.85 Ligands: 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: 8 residues within 4Å: Chain A: Y.159 Chain B: Y.188, W.218, R.257 Ligands: 3PE.3, DXC.7, DXC.8, DXC.11 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.257 Hydrophobic interactions: A:Y.159, A:Y.159, A:Y.159 DXC.11: 5 residues within 4Å: Chain B: T.258, L.259 Ligands: DXC.5, DXC.10, 3PE.14 No protein-ligand interaction detected (PLIP) DXC.15: 4 residues within 4Å: Chain B: M.160 Ligands: DXC.4, DXC.6, 3PE.14 No protein-ligand interaction detected (PLIP) DXC.16: 3 residues within 4Å: Chain B: R.82, L.259 Ligands: 3PE.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.82, B:L.259

1 x HCZ: 6-chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide 1,1-dioxide(Non-covalent)

HCZ.17: 7 residues within 4Å: Chain A: F.150, S.151, S.152, K.163 Chain B: S.151, S.152, N.194 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.152, A:S.152, B:S.152, B:R.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garau, G., MEMBRANE TARGET COMPLEX 1. 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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