SMTL ID : 8sl9.1

Crystal structure of Francisella tularensis HPPK-DHPS in complex with HPPK inhibitor HP-73

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x H73: 5'-S-[(2R,4R)-1-{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}-2-carboxypiperidin-4-yl]-5'-thioadenosine(Non-covalent)

H73.1: 29 residues within 4Å: Chain A: G.10, S.44, K.45, A.46, V.47, L.48, F.60, N.62, L.77, L.80, K.81, E.84, R.89, W.96, R.99, D.102, L.103, D.104, I.105, D.116, K.117, L.118, T.119, I.120, H.122, R.128, F.130 Ligands: EDO.7, EDO.9 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:W.96 Hydrogen bonds: A:S.44, A:V.47, A:V.47, A:N.62, A:N.62, A:K.81, A:R.99, A:D.102, A:D.102, A:I.105, A:I.105, A:K.117, A:T.119 Water bridges: A:R.99, A:T.119, A:K.123 Salt bridges: A:D.102, A:D.104, A:H.122, A:R.128 pi-Stacking: A:F.60, A:F.130 pi-Cation interactions: A:F.60, A:F.130

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

EDO.2: 7 residues within 4Å: Chain A: V.163, K.164, L.165, K.166, Q.204, I.248 Ligands: EDO.20 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: N.318, D.321, N.322, D.325 Ligands: EDO.5 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: D.151, I.154 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: D.321, D.325, R.372 Ligands: EDO.3, EDO.6 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: D.321, C.324, D.325, E.328, R.372, L.373 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: L.77, L.80, K.81, E.84, L.91, L.103, D.104 Ligands: H73.1 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: A.293, N.296, G.338, I.339, A.340, N.343 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: H.122, K.123 Ligands: H73.1 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: A.26, S.29, Q.30, L.79, D.82, I.83, K.86 Ligand excluded by PLIP EDO.11: 10 residues within 4Å: Chain A: Q.4, Y.5, I.6, K.66, A.107, A.108, E.109, L.135, S.139, W.142 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: F.15, I.274, W.275, Y.295, N.296, K.297 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: R.383, K.384, P.385, K.392, L.399 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: K.241, A.268, K.269, H.270, H.271, D.272, I.273 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: E.328, K.331, Q.332, L.335, Q.341, E.374 Ligands: EDO.18 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: E.368, R.371, R.372 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: I.367, K.370, L.413, D.414, I.415 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: Q.341, Q.342, E.374 Ligands: EDO.15 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: K.45, R.59, E.161, V.163, I.248 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: I.162, V.163, K.164 Ligands: EDO.2 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: V.47, N.127, R.128, S.129, F.130, L.159, E.161 Ligand excluded by PLIP EDO.22: 11 residues within 4Å: Chain A: I.177, D.347, L.378, G.380, H.381, S.382, K.384, R.419, V.420, H.421 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: I.177, N.179, T.217, K.384, R.419, H.421 Ligands: EDO.22 Ligand excluded by PLIP

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.24: 6 residues within 4Å: Chain A: A.39, S.40, L.41, T.168, L.169 Ligands: CL.26 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain A: W.142, H.143, W.150, D.151, L.152, N.153 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain A: K.38, T.168, L.169, A.170 Ligands: CL.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaw, G.X. et al., Crystal structure of Francisella tularensis HPPK-DHPS in complex with HPPK inhibitor HP-73. To be published

Release Date

2024-05-01

Peptides

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase