SMTL ID : 9cxo.1

Crystal structure of Human FN3K(D217S) mutant bound with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: P.253, G.254, F.255, D.256, Q.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.254, A:D.256, A:Q.257 PEG.6: 3 residues within 4Å: Chain B: E.61, R.64, R.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.64, B:R.64

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

SO4.2: 4 residues within 4Å: Chain A: A.1, M.2 Chain B: G.235, G.236 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.236, A:M.2 Water bridges: B:F.237, B:F.237 SO4.7: 4 residues within 4Å: Chain B: K.95, S.98, S.99, E.207 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.99, B:S.99, B:E.207 Water bridges: B:S.98 Salt bridges: B:K.95 SO4.8: 2 residues within 4Å: Chain B: R.177, L.290 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.177

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 18 residues within 4Å: Chain A: A.23, G.24, C.25, I.26, S.27, F.40, K.42, P.72, M.89, E.90, H.91, L.92, M.94, W.201, G.203, N.204, Y.215, D.216 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:C.25, A:I.26, A:S.27, A:E.90, A:L.92, A:W.201, A:G.203, A:N.204, A:D.216, A:D.216 Water bridges: A:D.216 Salt bridges: A:K.42, A:K.42 pi-Stacking: A:F.40, A:F.40 ATP.11: 21 residues within 4Å: Chain A: G.20, P.21 Chain B: A.23, G.24, C.25, I.26, S.27, F.40, K.42, P.72, M.89, E.90, H.91, L.92, M.94, W.201, G.203, N.204, Y.215, D.216 Ligands: EDO.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:C.25, B:I.26, B:S.27, B:E.90, B:L.92, B:W.201, B:G.203, B:Y.215, B:D.216 Water bridges: B:N.204, B:D.216 Salt bridges: B:K.42, B:K.42 pi-Stacking: B:F.40, B:F.40

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

EDO.4: 2 residues within 4Å: Chain A: H.128, W.142 No protein-ligand interaction detected (PLIP) EDO.5: 9 residues within 4Å: Chain A: G.19, P.21, R.30 Chain B: M.94, G.203, V.205, A.206, Y.215 Ligands: ATP.11 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.205, A:R.30, A:R.30 EDO.12: 4 residues within 4Å: Chain B: F.127, H.128, W.142, Y.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.128, B:Y.221 Water bridges: B:Y.221 EDO.13: 5 residues within 4Å: Chain B: F.127, V.130, V.139, N.140, E.141 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.128, B:N.140, B:E.141 EDO.14: 3 residues within 4Å: Chain B: Q.143, D.144, D.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.144, B:D.145 EDO.15: 5 residues within 4Å: Chain B: N.115, S.120, Y.121, V.122, V.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.120 EDO.16: 7 residues within 4Å: Chain B: H.112, L.113, Q.116, V.192, A.194, S.224, I.249 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.112, B:S.224 Water bridges: B:V.192, B:V.192

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

PO4.9: 8 residues within 4Å: Chain B: F.125, D.144, D.145, W.146, P.147, L.189, E.190, I.191 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.144, B:D.144, B:D.145, B:W.146, B:E.190, B:I.191 PO4.10: 3 residues within 4Å: Chain B: H.246, P.250, K.251 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.251 Salt bridges: B:K.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garg, A. et al., The molecular basis of Human FN3K mediated phosphorylation of glycated substrates. Nat Commun (2025)

Release Date

2024-12-18

Peptides

Fructosamine-3-kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fructosamine-3-kinase