SMTL ID : 8gkc.1

Atomic model of the core modifying region of human fatty acid synthase in complex with TVB-2640 - C2 refinement

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x X5O: denifanstat(Non-covalent)

X5O.1: 19 residues within 4Å: Chain A: L.1122, D.1124, S.1168, V.1169, S.1170, R.1173, G.1174, N.1175, A.1176, Q.1178, Y.1181, W.1207, I.1215, L.1216, T.1219, V.1227, S.1228, T.1230 Ligands: NDP.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.1122, A:V.1169, A:V.1169, A:I.1215, A:L.1216, A:T.1219, A:V.1227, A:T.1230 Hydrogen bonds: A:D.1124, A:S.1168, A:S.1170, A:R.1173, A:N.1175 X5O.4: 20 residues within 4Å: Chain B: L.1122, D.1124, S.1168, V.1169, S.1170, R.1173, G.1174, N.1175, A.1176, Q.1178, Y.1181, W.1207, G.1208, I.1215, L.1216, T.1219, V.1227, S.1228, T.1230 Ligands: NDP.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.1122, B:V.1169, B:V.1169, B:I.1215, B:L.1216, B:T.1219, B:V.1227, B:T.1230 Hydrogen bonds: B:D.1124, B:S.1168, B:S.1170, B:R.1173, B:N.1175

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 25 residues within 4Å: Chain A: F.720, V.798, T.801, S.822, S.824, G.825, G.826, V.827, G.828, V.846, G.847, K.851, S.870, R.871, I.916, K.918, V.941, L.942, L.943, M.990, A.991, Q.992, G.993, H.995, G.997 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.801 Hydrogen bonds: A:S.822, A:S.822, A:S.824, A:S.824, A:G.826, A:V.827, A:G.828, A:G.847, A:K.851, A:S.870, A:V.941, A:L.943, A:M.990, A:G.997 Salt bridges: A:K.851, A:R.871, A:H.995 pi-Stacking: A:H.995 NDP.3: 30 residues within 4Å: Chain A: G.1038, L.1040, G.1041, G.1042, F.1043, T.1062, S.1063, R.1064, S.1065, R.1068, N.1092, N.1117, L.1118, A.1119, V.1120, V.1121, P.1141, K.1142, F.1166, S.1167, S.1168, Y.1181, W.1207, G.1208, A.1209, I.1210, G.1214, I.1215, L.1216 Ligands: X5O.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.1207, A:I.1210 Hydrogen bonds: A:G.1038, A:L.1040, A:G.1042, A:F.1043, A:S.1063, A:R.1064, A:S.1065, A:N.1092, A:N.1092, A:L.1118, A:V.1120, A:K.1142, A:K.1142, A:Y.1181, A:I.1210, A:I.1215 Salt bridges: A:R.1064 NDP.5: 26 residues within 4Å: Chain B: F.720, V.798, T.801, S.822, S.824, G.825, G.826, V.827, G.828, V.846, G.847, K.851, S.870, R.871, S.894, I.916, K.918, V.941, L.942, L.943, M.990, A.991, Q.992, G.993, H.995, G.997 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:T.801, B:I.916 Hydrogen bonds: B:S.822, B:S.822, B:S.824, B:S.824, B:G.826, B:V.827, B:G.828, B:G.847, B:K.851, B:S.870, B:V.941, B:L.943, B:M.990, B:G.997 Salt bridges: B:K.851, B:R.871, B:H.995 pi-Stacking: B:H.995 NDP.6: 29 residues within 4Å: Chain B: G.1038, L.1040, G.1041, G.1042, F.1043, T.1062, S.1063, R.1064, S.1065, N.1092, N.1117, L.1118, A.1119, V.1120, V.1121, P.1141, K.1142, F.1166, S.1167, S.1168, Y.1181, W.1207, G.1208, A.1209, I.1210, G.1214, I.1215, L.1216 Ligands: X5O.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.1207, B:I.1210 Hydrogen bonds: B:G.1038, B:L.1040, B:G.1042, B:F.1043, B:S.1063, B:R.1064, B:S.1065, B:N.1092, B:N.1092, B:L.1118, B:V.1120, B:K.1142, B:K.1142, B:Y.1181, B:I.1210, B:I.1215 Salt bridges: B:R.1064

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasan, S.M.N. et al., Atomic model for core modifying region of human fatty acid synthase in complex with Denifanstat. Nat Commun (2023)

Release Date

2023-05-24

Peptides

Fatty acid synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Fatty acid synthase

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