SMTL ID : 8ce3.1

Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 3D fragment 2548

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: F.344, E.380, F.503, K.505, G.506 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.380, A:G.506 EDO.2: 3 residues within 4Å: Chain A: H.244, K.266 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: F.160, S.319, I.326, G.327, K.328, T.330 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.327, A:K.328 EDO.12: 6 residues within 4Å: Chain A: N.221, H.244, Y.246, M.247, E.248 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.244, A:Y.246 EDO.13: 1 residues within 4Å: Chain A: I.217 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain A: F.154, W.175, K.328 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: H.171, K.172, T.173 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.172, A:T.173

1 x UE0: (3~{S})-1-ethanoyl-3-(4-methylphenyl)piperidine-3-carboxylic acid(Non-covalent)

UE0.3: 14 residues within 4Å: Chain A: F.77, S.78, L.82, Y.226, K.228, T.252, Y.254, L.271, S.272, L.276, L.280, F.286, A.297, E.300 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.82, A:Y.254, A:L.276, A:L.280, A:A.297 Hydrogen bonds: A:K.228 Water bridges: A:Y.226, A:T.252 Salt bridges: A:K.228

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

SO4.4: 4 residues within 4Å: Chain A: R.31, G.273, R.274 Chain B: R.274 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.274, A:R.274 Salt bridges: B:R.274, A:R.31 SO4.5: 4 residues within 4Å: Chain A: K.134, G.176, K.177, W.178 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.134, A:G.176, A:W.178 Salt bridges: A:K.134 SO4.6: 3 residues within 4Å: Chain A: K.56, R.103, G.117 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.56, A:R.103 SO4.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.9: 2 residues within 4Å: Chain A: K.317, N.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.356 Water bridges: A:K.236 Salt bridges: A:K.317 SO4.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.16: 5 residues within 4Å: Chain A: K.266 Chain B: K.17, K.18, R.23, R.26 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.266, B:K.17, B:R.23, B:R.26 Hydrogen bonds: B:K.18 SO4.17: 4 residues within 4Å: Chain B: K.134, G.176, K.177, W.178 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.134 SO4.18: 1 residues within 4Å: Chain B: N.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.48 SO4.19: 1 residues within 4Å: Chain B: K.317 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.317 SO4.20: 1 residues within 4Å: Chain B: E.50 No protein-ligand interaction detected (PLIP) SO4.21: 5 residues within 4Å: Chain B: T.65, K.66, E.67, S.107, L.108 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.66, B:E.67, B:E.67, B:L.108 Water bridges: B:S.107, B:A.109 Salt bridges: B:K.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Downes, T.D. et al., A Modular 3-D Fragment Collection: Design, Synthesis and Screening. To Be Published

Release Date

2024-02-21

Peptides

Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A

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