SMTL ID : 9cxv.1

Crystal structure of Human FN3K bound with ADP and DMF (I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: G.67, L.68, V.69, R.70, Q.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.69, A:Q.107 Water bridges: A:R.70 SO4.2: 2 residues within 4Å: Chain A: R.177, L.290 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.181, A:K.181 Salt bridges: A:R.177 SO4.12: 5 residues within 4Å: Chain B: A.1, M.2, E.3, G.235, G.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.2, B:E.3, B:G.236 Water bridges: B:Q.4

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: N.204, D.216 Ligands: ADP.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.216, H2O.1, H2O.6

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

EDO.4: 4 residues within 4Å: Chain A: V.57, P.74, M.75, V.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.74 Water bridges: A:V.77 EDO.5: 6 residues within 4Å: Chain A: H.112, L.113, A.194, S.224, I.249 Ligands: EDO.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.112, A:S.224 Water bridges: A:E.190, A:V.192, A:V.192, A:V.192, A:H.223 EDO.6: 4 residues within 4Å: Chain A: Q.116, E.190, V.192 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.116, A:E.190 Water bridges: A:P.250 EDO.7: 8 residues within 4Å: Chain A: F.127, H.128, T.129, V.130, Q.138, V.139, N.140, E.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.128, A:N.140, A:E.141 EDO.10: 2 residues within 4Å: Chain A: T.47 Chain B: S.280 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.280, A:T.47, A:T.47 Water bridges: B:S.280 EDO.11: 4 residues within 4Å: Chain A: K.95, S.96 Chain B: G.22, R.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.22, B:R.30, B:R.30 EDO.13: 3 residues within 4Å: Chain A: A.1, M.2 Chain B: R.45 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.45, B:R.45, A:M.2 EDO.14: 4 residues within 4Å: Chain B: H.112, 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:S.224 EDO.15: 2 residues within 4Å: Chain B: P.238, R.239 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.237 EDO.16: 5 residues within 4Å: Chain B: K.251, A.252, G.254, F.255, D.256 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.252, B:G.254, B:D.256, B:D.256 EDO.18: 3 residues within 4Å: Chain B: D.184, C.187, G.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.184, B:C.187 Water bridges: B:G.188 EDO.20: 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

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.8: 16 residues within 4Å: Chain A: I.26, S.27, E.28, F.40, K.42, P.72, M.89, E.90, H.91, L.92, M.94, G.203, N.204, Y.215, D.216 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:I.26, A:E.90, A:L.92, A:G.203, A:Y.215 Water bridges: A:K.42, A:N.204 Salt bridges: A:K.42, A:K.42 pi-Stacking: A:F.40, A:F.40 ADP.17: 18 residues within 4Å: Chain B: G.19, 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, G.203, N.204, Y.215, D.216 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.19, B:C.25, B:I.26, B:S.27, B:E.90, B:L.92, B:G.203, B:D.216, B:D.216 Water bridges: B:N.204, B:N.204, B:Y.215, B:D.216, B:D.216, B:D.216 Salt bridges: B:K.42, B:K.42 pi-Stacking: B:F.40, B:F.40

2 x 01: 1-deoxy-1-(morpholin-4-yl)-D-fructose

01.9: 10 residues within 4Å: Chain A: C.133, G.134, D.199, W.201, I.230, F.234, N.269, H.270, H.273, F.274 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.199, A:H.270 Water bridges: A:N.204, A:D.216, A:H.270 pi-Cation interactions: A:W.201, A:W.201 01.19: 14 residues within 4Å: Chain A: S.27 Chain B: C.25, I.26, G.134, D.199, W.201, N.204, D.216, I.230, F.234, N.269, H.270, H.273, F.274 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.199, B:N.204, B:D.216, B:H.270, B:H.273, A:S.27 Water bridges: B:D.199, B:D.216, B:N.269, B:N.269, B:N.269 pi-Cation interactions: B:W.201, B:W.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garg, A. et al., Crystal structure of Human FN3K bound with ADP and DMF (I). To Be Published

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

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