SMTL ID : 7aia.1

Complex of human GDAP1 with hexadecanedioic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: D.178, N.179, Y.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.179 GOL.2: 10 residues within 4Å: Chain A: P.89, Y.95, V.99, W.216, C.218, G.219, E.220, S.221, T.223 Ligands: EOH.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.220, A:S.221, A:S.221 Water bridges: A:T.223 GOL.3: 3 residues within 4Å: Chain A: S.93, M.94, Y.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.94 GOL.5: 3 residues within 4Å: Chain A: N.276, I.277, L.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.276, A:N.276 Water bridges: A:I.277 GOL.6: 7 residues within 4Å: Chain A: E.1, V.2, K.3, L.4, L.27, K.28, F.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.28 Water bridges: A:L.4 GOL.11: 8 residues within 4Å: Chain A: H.11, S.12, F.13, S.14, L.49, N.50, D.112, R.235 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.12, A:F.13, A:S.14, A:R.235 Water bridges: A:T.115

6 x EOH: ETHANOL(Non-functional Binders)

EOH.4: 7 residues within 4Å: Chain A: R.86, L.87, M.88, P.89, S.221, T.223 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.223 Hydrogen bonds: A:R.86 EOH.7: 5 residues within 4Å: Chain A: T.256, E.259, R.260, K.263 Ligands: EOH.9 No protein-ligand interaction detected (PLIP) EOH.8: 4 residues within 4Å: Chain A: L.174, H.177, D.178, K.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.181 EOH.9: 6 residues within 4Å: Chain A: G.212, Q.213, Q.214, R.260 Ligands: EOH.7, RF8.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.214 Hydrogen bonds: A:Q.214 EOH.10: 4 residues within 4Å: Chain A: T.125, V.126, D.127, S.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.125, A:D.127, A:S.128 EOH.12: 5 residues within 4Å: Chain A: S.108, L.109, P.110, E.189, V.193 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.189 Hydrogen bonds: A:S.108 Water bridges: A:E.189

1 x RF8: hexadecanedioic acid(Non-covalent)

RF8.13: 11 residues within 4Å: Chain A: E.24, Q.213, Q.214, W.216, S.221, F.222, R.260, R.264, K.265, T.266 Ligands: EOH.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.216, A:K.265 Hydrogen bonds: A:Q.213, A:K.265 Water bridges: A:R.264, A:R.264 Salt bridges: A:R.260, A:R.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, G.T.T. et al., Structure of the Complete Dimeric Human GDAP1 Core Domain Provides Insights into Ligand Binding and Clustering of Disease Mutations. Front Mol Biosci (2020)

Release Date

2021-02-24

Peptides

Ganglioside-induced differentiation-associated protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Ganglioside-induced differentiation-associated protein 1

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