SMTL ID : 9cxm.1

Crystal structure of Human FN3K bound with ATP and DMF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 1 residues within 4Å: Chain A: R.177 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.177 SO4.12: 5 residues within 4Å: Chain A: R.45 Chain B: A.1, M.2, G.235, G.236 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.2, B:G.236, A:R.45 SO4.13: 2 residues within 4Å: Chain B: P.238, R.239 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.239 Water bridges: B:Q.4, B:S.240

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

EDO.2: 4 residues within 4Å: Chain A: V.57, P.74, M.75, V.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.74 Water bridges: A:R.50, A:V.77 EDO.3: 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.4: 3 residues within 4Å: Chain A: R.239, S.240, T.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.243 EDO.5: 4 residues within 4Å: Chain A: E.170, R.279, S.280, R.287 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.279, A:S.280, A:R.287 Water bridges: A:R.287 EDO.6: 5 residues within 4Å: Chain A: G.67, L.68, V.69, R.70, Q.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.107 Water bridges: A:V.69 EDO.7: 4 residues within 4Å: Chain A: V.122, D.123, K.124, W.142 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: G.20, K.95, S.96 Chain B: G.22, R.30 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.22, A:S.96 EDO.10: 6 residues within 4Å: Chain A: H.112, L.113, Q.116, A.194, S.224, I.249 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.112, A:S.224 Water bridges: A:V.192, A:V.192, A:V.192, A:H.223 EDO.11: 3 residues within 4Å: Chain A: G.254, F.255, D.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.254, A:D.256 EDO.14: 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.17: 6 residues within 4Å: Chain B: H.112, L.113, Q.116, A.194, S.224, I.249 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.112, B:Q.116, B:S.224 Water bridges: B:V.192, B:H.223, B:S.224, B:E.225 EDO.18: 2 residues within 4Å: Chain B: R.177, R.287 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.177, B:R.287, B:R.287 Water bridges: B:R.177 EDO.19: 2 residues within 4Å: Chain B: R.279, S.280 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.279 Water bridges: B:S.280, B:S.280 EDO.20: 3 residues within 4Å: Chain B: D.123, K.124, D.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.144 EDO.21: 6 residues within 4Å: Chain B: N.115, S.120, Y.121, V.122, D.123, V.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.120

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

ADP.8: 12 residues within 4Å: Chain A: S.27, F.40, K.42, P.72, M.89, E.90, H.91, L.92, M.94, N.204, Y.215, D.216 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.27, A:E.90, A:L.92, A:G.203, A:Y.215, A:D.216 Water bridges: A:S.27, A:N.204, A:N.204 Salt bridges: A:K.42, A:K.42 pi-Stacking: A:F.40, A:F.40

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

ATP.15: 19 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, W.201, G.203, N.204, Y.215, D.216 Ligands: 01.16 17 PLIP interactions: 17 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:W.201, B:G.203, B:N.204, B:D.216, B:D.216 Water bridges: B:D.199, B:D.216 Salt bridges: B:K.42, B:K.42 pi-Stacking: B:F.40, B:F.40

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

01.16: 14 residues within 4Å: Chain B: C.25, I.26, C.133, G.134, D.199, W.201, N.204, D.216, F.234, N.269, H.270, H.273, F.274 Ligands: ATP.15 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.134, B:D.199, B:W.201, B:N.204, B:N.269, B:H.270 Water bridges: B:D.199, B:D.199, B:D.199, B:D.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garg, A. et al., Crystal structure of Human FN3K bound with ATP and DMF. 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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