SMTL ID : 9cxn.1

Crystal structure of Human FN3K bound with AMPPNP and DMF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: P.238, R.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.239 Water bridges: A:S.240 SO4.2: 1 residues within 4Å: Chain A: R.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.177 Salt bridges: A:R.177 SO4.11: 5 residues within 4Å: Chain B: A.1, M.2, E.3, G.235, G.236 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:M.2, B:E.3, B:E.3, B:E.3, B:G.236 Water bridges: B:Q.4

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

EDO.3: 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, A:V.77 Water bridges: A:R.50 EDO.4: 3 residues within 4Å: Chain A: A.1, M.2 Chain B: R.45 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.2, B:R.45, B:R.45 Water bridges: A:E.3, A:E.3 EDO.5: 3 residues within 4Å: Chain A: V.122, K.124, W.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.123 EDO.7: 3 residues within 4Å: Chain A: E.170, R.279, R.287 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.170, A:R.279, A:R.287 Water bridges: A:S.280, A:S.280 EDO.9: 2 residues within 4Å: Chain A: K.95, S.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.96 EDO.10: 5 residues within 4Å: Chain A: H.112, L.113, A.194, S.224, I.249 7 PLIP interactions: 7 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, A:S.224 EDO.12: 6 residues within 4Å: Chain B: K.251, A.252, P.253, G.254, F.255, D.256 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.252, B:G.254, B:F.255, B:D.256, B:D.256 EDO.14: 4 residues within 4Å: Chain B: N.115, S.120, Y.121, V.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.121 EDO.15: 1 residues within 4Å: Chain B: E.173 No protein-ligand interaction detected (PLIP) EDO.16: 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:A.1, B:A.1

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 14 residues within 4Å: Chain A: 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.28, A:E.28, A:K.42, A:E.90, A:L.92, A:G.203, A:Y.215, A:D.216 Water bridges: A:K.42, A:N.204, A:D.216 Salt bridges: A:K.42 pi-Stacking: A:F.40 ANP.13: 22 residues within 4Å: Chain A: G.22, A.23, G.24 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 Ligands: 01.17 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.19, B:C.25, B:I.26, B:S.27, B:K.42, B:E.90, B:L.92, B:G.203, B:D.216, A:A.23 Water bridges: B:S.27, B:S.27, B:N.204 Salt bridges: B:K.42 pi-Stacking: B:F.40, B:F.40

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

01.8: 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:N.204, A:H.270 pi-Cation interactions: A:W.201, A:W.201 01.17: 14 residues within 4Å: Chain A: C.25, S.27 Chain B: I.26, G.134, D.199, W.201, N.204, I.230, F.234, N.269, H.270, H.273, F.274 Ligands: ANP.13 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.199, B:N.204, B:D.216, B:N.269, B:H.270, B:H.273, A:S.27 Water bridges: B:D.216 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 AMPPNP 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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