SMTL ID : 7ndw.1

ThyX-FADH2 soaked with 20 mM Formaldehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

2 x HUF: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate(Non-covalent)

HUF.1: 23 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain C: S.42, T.67, E.70, I.93, N.175, R.177 Chain D: S.95, N.97, E.98, S.100, R.102, Y.103 Ligands: FDA.7, PG4.9, PO4.11 27 PLIP interactions: 5 interactions with chain C, 6 interactions with chain D, 16 interactions with chain A Hydrogen bonds: C:T.67, C:N.175, D:A.94, D:E.98, D:E.98, A:R.90, A:R.90, A:R.92, A:R.92, A:I.93, A:N.181, A:N.181 Water bridges: C:S.42, C:E.66, D:Y.96, D:E.98, D:E.98, A:R.90, A:H.91, A:H.91, A:R.186 Salt bridges: C:R.177, A:H.91, A:H.91, A:R.92, A:R.92 Hydrophobic interactions: A:L.185 HUF.3: 26 residues within 4Å: Chain B: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Chain C: A.94, S.95, N.97, E.98, S.100, Y.103 Chain D: S.42, T.67, E.70, I.93, N.175, R.177 Ligands: PEG.6, PO4.8, FDA.10, PEG.12, PEG.14 21 PLIP interactions: 13 interactions with chain B, 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: B:L.185 Hydrogen bonds: B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, D:T.67, D:N.175, C:S.95, C:E.98, C:E.98 Water bridges: B:R.186, D:S.42, C:R.102 Salt bridges: B:H.91, B:H.91, B:R.92, B:R.92, D:R.177

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: K.62, H.63, Y.220 No protein-ligand interaction detected (PLIP) PEG.5: 9 residues within 4Å: Chain B: L.18, D.19, Y.111, I.112, P.113, S.114, E.116, R.117, W.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.111, B:S.114 PEG.6: 8 residues within 4Å: Chain B: E.66, R.177, M.180, N.181, N.184 Ligands: HUF.3, FDA.10, PEG.14 No protein-ligand interaction detected (PLIP) PEG.12: 6 residues within 4Å: Chain B: L.185 Chain D: G.64, H.65, E.66, T.67 Ligands: HUF.3 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.65, D:E.66 PEG.13: 8 residues within 4Å: Chain A: I.82, L.99, G.101, R.159, L.166, T.168 Chain D: R.86, L.164 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:T.168, A:T.168, D:R.86, D:R.86 PEG.14: 7 residues within 4Å: Chain D: E.66, R.177, M.180, N.181, A.221 Ligands: HUF.3, PEG.6 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.184 PEG.15: 6 residues within 4Å: Chain D: D.19, K.20, Y.108, E.109, F.110, I.112 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.20, D:F.110, D:F.110

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain B: S.100, G.101, R.102, R.159 Chain C: Q.87 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.101, B:R.102, C:Q.87 Water bridges: B:R.159, B:R.159 Salt bridges: B:R.159 PO4.8: 6 residues within 4Å: Chain B: Q.87 Chain C: S.100, G.101, R.102, R.159 Ligands: HUF.3 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:G.101, C:R.102, B:Q.87 Water bridges: C:L.99, C:R.159, C:R.159, B:R.86, B:R.86 Salt bridges: C:R.159 PO4.11: 6 residues within 4Å: Chain A: Q.87 Chain D: S.100, G.101, R.102, R.159 Ligands: HUF.1 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:Q.87, D:S.100, D:G.101, D:R.102 Water bridges: A:R.90, D:R.159, D:R.159 Salt bridges: D:R.159

2 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.7: 21 residues within 4Å: Chain A: T.67, E.70, I.93, N.175, R.177 Chain B: A.94, S.95, N.97, E.98, S.100, R.102 Chain C: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Ligands: HUF.1 20 PLIP interactions: 14 interactions with chain C, 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:L.185 Hydrogen bonds: C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, B:S.95, B:E.98, B:E.98, A:N.175 Water bridges: C:R.90, C:R.186, B:Y.96 Salt bridges: C:H.91, C:H.91, C:R.92, C:R.92, A:R.177 FDA.10: 22 residues within 4Å: Chain A: A.94, S.95, N.97, E.98, S.100 Chain B: H.63, G.64, H.65, T.67, E.70, I.93, N.175, R.177 Chain D: R.90, H.91, R.92, I.93, N.181, L.185, R.186 Ligands: HUF.3, PEG.6 28 PLIP interactions: 16 interactions with chain D, 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: D:L.185, B:H.65 Hydrogen bonds: D:R.90, D:R.90, D:R.92, D:R.92, D:I.93, D:N.181, D:N.181, D:R.186, A:A.94, A:E.98, A:E.98, B:N.175, B:R.177 Water bridges: D:R.90, D:H.91, D:H.91, A:A.94, A:Y.96, B:R.177 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, B:R.177 pi-Stacking: B:H.65, B:H.65

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 13 residues within 4Å: Chain A: L.185 Chain C: A.39, S.42, F.43, L.60, G.64, H.65, E.66, T.67, P.68 Chain D: N.97, Y.103 Ligands: HUF.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.42, C:E.66, C:T.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bou-Nader, C. et al., An enzymatic activation of formaldehyde for nucleotide methylation. Nat Commun (2021)

Release Date

2021-07-21

Peptides

Flavin-dependent thymidylate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Flavin-dependent thymidylate synthase

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