SMTL ID : 9iit.1

Full length structure of FKP in complex with GTP and GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 18 residues within 4Å: Chain A: S.26, D.51, K.56, L.57, G.58, S.59, G.62, H.93, A.94, G.95, G.96, Q.97, S.98, R.99, R.100, K.109, S.154, D.156 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.26, A:S.26, A:L.57, A:G.58, A:G.95, A:G.96, A:Q.97, A:S.98, A:S.98, A:R.99, A:R.99, A:R.100, A:R.100, A:D.156 Salt bridges: A:D.51, A:R.100, A:K.109, A:K.109, A:K.109 GTP.2: 13 residues within 4Å: Chain A: P.115, V.116, L.125, K.320, V.329, Q.330, N.331, A.332, N.506, A.509, L.510, N.513, S.517 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.116, A:L.125, A:N.331, A:N.331, A:N.331, A:A.332, A:N.506, A:N.513 Water bridges: A:V.329, A:A.332, A:R.503 Salt bridges: A:K.320, A:K.320, A:K.320 GTP.8: 15 residues within 4Å: Chain B: S.26, D.51, K.56, L.57, G.58, H.93, A.94, G.95, G.96, Q.97, S.98, R.99, R.100, K.109, D.156 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.26, B:S.26, B:L.57, B:G.58, B:H.93, B:G.96, B:Q.97, B:S.98, B:S.98, B:R.99, B:R.99, B:R.100, B:D.156, B:D.156 Water bridges: B:D.51 Salt bridges: B:D.51, B:K.109, B:K.109, B:K.109 GTP.14: 18 residues within 4Å: Chain C: S.26, D.51, K.56, L.57, G.58, S.59, G.62, H.93, A.94, G.95, G.96, Q.97, S.98, R.99, R.100, K.109, S.154, D.156 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:S.26, C:S.26, C:D.51, C:L.57, C:G.58, C:H.93, C:G.95, C:G.96, C:Q.97, C:S.98, C:S.98, C:R.99, C:R.99, C:R.100, C:R.100, C:D.156 Salt bridges: C:D.51, C:R.100, C:K.109, C:K.109, C:K.109 GTP.15: 13 residues within 4Å: Chain C: P.115, V.116, L.125, K.320, V.329, Q.330, N.331, A.332, N.506, A.509, L.510, N.513, S.517 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.116, C:L.125, C:N.331, C:N.331, C:N.331, C:A.332, C:N.506, C:N.513 Water bridges: C:V.329, C:A.332, C:R.503 Salt bridges: C:K.320, C:K.320, C:K.320 GTP.21: 15 residues within 4Å: Chain D: S.26, D.51, K.56, L.57, G.58, H.93, A.94, G.95, G.96, Q.97, S.98, R.99, R.100, K.109, D.156 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.26, D:S.26, D:L.57, D:G.58, D:G.96, D:Q.97, D:S.98, D:S.98, D:R.99, D:R.99, D:R.100, D:D.156, D:D.156 Salt bridges: D:D.51, D:K.109, D:K.109, D:K.109

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 3 residues within 4Å: Chain A: A.525, R.560, S.844 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.560, A:R.560, A:S.849 Water bridges: A:E.529 FMT.4: 2 residues within 4Å: Chain A: D.679, K.681 No protein-ligand interaction detected (PLIP) FMT.16: 3 residues within 4Å: Chain C: A.525, R.560, S.844 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.560, C:R.560, C:S.849 FMT.17: 2 residues within 4Å: Chain C: D.679, K.681 No protein-ligand interaction detected (PLIP)

2 x MLA: MALONIC ACID(Non-covalent)

MLA.5: 8 residues within 4Å: Chain A: A.732, G.733, S.734, G.735, L.736, G.737, T.738, S.739 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.733, A:S.734, A:G.735, A:L.736, A:G.737, A:T.738, A:S.739, A:S.739 Water bridges: A:S.740 MLA.18: 8 residues within 4Å: Chain C: A.732, G.733, S.734, G.735, L.736, G.737, T.738, S.739 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.733, C:S.734, C:G.735, C:L.736, C:G.737, C:T.738, C:S.739, C:S.739 Water bridges: C:S.740

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: S.662, D.664, M.665, P.686, F.687, P.690, L.726, A.728, L.742 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.664 Water bridges: A:I.689 GOL.7: 9 residues within 4Å: Chain A: R.612, G.618, W.619, D.621, T.622, Q.781, D.782, G.919, A.920 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.612, A:W.619, A:D.621, A:Q.781, A:D.782 Water bridges: A:Q.781, A:A.920 GOL.12: 4 residues within 4Å: Chain B: H.188, G.189, D.225, Y.257 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.189, B:D.225, B:D.225 Water bridges: B:S.154, B:S.154 GOL.13: 8 residues within 4Å: Chain B: S.662, D.664, P.686, F.687, P.690, L.726, A.728, L.742 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.686, B:L.726 GOL.19: 9 residues within 4Å: Chain C: S.662, D.664, M.665, P.686, F.687, P.690, L.726, A.728, L.742 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.664 Water bridges: C:I.689 GOL.20: 9 residues within 4Å: Chain C: R.612, G.618, W.619, D.621, T.622, Q.781, D.782, G.919, A.920 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.612, C:W.619, C:D.621, C:Q.781, C:D.782 Water bridges: C:Q.781, C:A.920 GOL.25: 4 residues within 4Å: Chain D: H.188, G.189, D.225, Y.257 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.189, D:D.225, D:D.225 Water bridges: D:S.154, D:S.154 GOL.26: 8 residues within 4Å: Chain D: S.662, D.664, P.686, F.687, P.690, L.726, A.728, L.742 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.686, D:L.726

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.9: 14 residues within 4Å: Chain B: P.115, V.116, L.125, K.320, K.322, V.329, Q.330, N.331, A.332, N.506, A.509, L.510, N.513, S.517 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:V.116, B:L.125, B:N.331, B:N.331, B:N.331, B:A.332, B:N.506, B:N.513 Water bridges: B:A.332, B:R.503 Salt bridges: B:K.320, B:K.320, B:K.322 GDP.22: 14 residues within 4Å: Chain D: P.115, V.116, L.125, K.320, K.322, V.329, Q.330, N.331, A.332, N.506, A.509, L.510, N.513, S.517 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:V.116, D:L.125, D:N.331, D:N.331, D:N.331, D:A.332, D:N.506, D:N.513 Water bridges: D:A.332, D:R.503 Salt bridges: D:K.320, D:K.320, D:K.322

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 5 residues within 4Å: Chain B: Q.200, L.201, G.265, S.279, V.280 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.201, B:V.280 ACT.11: 3 residues within 4Å: Chain B: E.39, W.46, L.130 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.130 Hydrogen bonds: B:E.39 ACT.23: 5 residues within 4Å: Chain D: Q.200, L.201, G.265, S.279, V.280 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.201, D:V.280 ACT.24: 3 residues within 4Å: Chain D: E.39, W.46, L.130 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, S.W. et al., Structural insight into the catalytic mechanism of the bifunctional enzyme l-fucokinase/GDP-fucose pyrophosphorylase. J.Biol.Chem. (2025)

Release Date

2025-03-05

Peptides

L-fucokinase/L-fucose-1-P guanylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-fucokinase/L-fucose-1-P guanylyltransferase