SMTL ID : 5g3w.1

Structure of HDAC like protein from Bordetella Alcaligenes in complex with the photoswitchable inhibitor CEW65

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.185, H.187, D.273 Ligands: C65.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.185, A:D.185, A:H.187, A:D.273 ZN.8: 5 residues within 4Å: Chain B: H.147, D.185, H.187, D.273 Ligands: C65.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.185, B:D.185, B:H.187, B:D.273 ZN.16: 4 residues within 4Å: Chain C: D.185, H.187, D.273 Ligands: C65.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.185, C:D.185, C:H.187, C:D.273 ZN.23: 4 residues within 4Å: Chain D: D.185, H.187, D.273 Ligands: C65.26 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.185, D:D.185, D:H.187, D:D.273

8 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: D.183, D.185, H.187, G.189, S.206, L.207, H.208 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.185, A:H.187, A:S.206, A:L.207 K.3: 5 residues within 4Å: Chain A: W.196, D.199, V.202, T.204, Y.231 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.199, A:V.202, A:Y.231, H2O.14, H2O.14 K.9: 6 residues within 4Å: Chain B: D.183, D.185, H.187, S.206, L.207, H.208 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.183, B:D.185, B:H.187, B:S.206, B:L.207 K.10: 5 residues within 4Å: Chain B: W.196, D.199, V.202, T.204, Y.231 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.199, B:V.202, B:Y.231, H2O.30, H2O.31 K.17: 6 residues within 4Å: Chain C: D.183, D.185, H.187, S.206, L.207, H.208 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.183, C:D.185, C:H.187, C:S.206, C:L.207 K.18: 5 residues within 4Å: Chain C: W.196, D.199, V.202, T.204, Y.231 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.199, C:V.202, C:Y.231, H2O.48, H2O.48 K.24: 5 residues within 4Å: Chain D: W.196, D.199, V.202, T.204, Y.231 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.199, D:V.202, D:Y.231, H2O.63, H2O.64 K.25: 6 residues within 4Å: Chain D: D.183, D.185, H.187, G.189, S.206, L.207 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.183, D:D.185, D:H.187, D:S.206, D:L.207

11 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: L.355, L.356, D.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.357 Water bridges: A:A.358, A:R.360 PEG.5: 4 residues within 4Å: Chain A: L.174, G.175, M.176, Q.264 No protein-ligand interaction detected (PLIP) PEG.6: 3 residues within 4Å: Chain A: E.177, R.178, P.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.177, A:E.177, A:R.178 PEG.11: 5 residues within 4Å: Chain B: E.177, R.178, P.200, N.227, Y.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.177 Water bridges: B:Y.231 PEG.13: 4 residues within 4Å: Chain B: T.101, G.102, N.152, A.153 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.88, B:N.152, B:N.152 PEG.14: 6 residues within 4Å: Chain B: R.91, V.92, L.95, D.100, T.101, G.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.91, B:R.91, B:D.100 PEG.20: 5 residues within 4Å: Chain C: Q.193, W.197, D.216, S.217, E.222 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.193, C:D.216 PEG.22: 4 residues within 4Å: Chain C: D.194, W.197, N.198, A.225 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.194, C:N.198 Water bridges: C:W.197 PEG.27: 3 residues within 4Å: Chain D: R.178, P.200, Y.231 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.178 Water bridges: D:N.227 PEG.28: 4 residues within 4Å: Chain D: Q.193, W.197, D.216, E.222 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.193, D:D.216 PEG.29: 5 residues within 4Å: Chain D: K.90, S.93, N.94, G.111, L.113 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.93, D:N.94, D:G.111 Water bridges: D:E.114

4 x C65: (2E)-N-hydroxy-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-enamide(Non-covalent)

C65.7: 16 residues within 4Å: Chain A: L.26, I.105, H.147, H.148, G.156, F.157, D.185, H.187, F.213, D.273, G.315, Y.317 Chain B: P.342, Y.343, F.346 Ligands: ZN.1 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:Y.343, B:F.346, B:F.346, B:F.346, B:F.346, A:L.26, A:L.26, A:I.105, A:I.105, A:F.157, A:F.157, A:F.157, A:F.213 pi-Stacking: A:H.187, A:F.213 C65.15: 14 residues within 4Å: Chain A: F.346 Chain B: L.26, I.105, H.147, H.148, F.157, D.185, H.187, F.213, D.273, L.280, G.315, Y.317 Ligands: ZN.8 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.26, B:L.26, B:I.105, B:I.105, B:F.157, B:F.157, B:F.213, B:F.213, B:L.280, B:Y.317, A:F.346, A:F.346, A:F.346, A:F.346 C65.19: 13 residues within 4Å: Chain C: L.26, I.105, H.147, H.148, G.156, D.185, H.187, F.213, D.273, G.315, Y.317 Chain D: F.346 Ligands: ZN.16 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.26, C:L.26, C:I.105, C:F.213, C:F.213, D:F.346, D:F.346 Hydrogen bonds: C:Y.317 pi-Stacking: C:F.157 C65.26: 15 residues within 4Å: Chain C: Y.343, F.346 Chain D: L.26, I.105, H.147, H.148, F.157, D.185, H.187, F.213, D.273, L.280, G.315, Y.317 Ligands: ZN.23 16 PLIP interactions: 11 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.26, D:L.26, D:I.105, D:I.105, D:F.157, D:F.157, D:F.213, D:F.213, D:L.280, D:Y.317, C:Y.343, C:F.346, C:F.346, C:F.346, C:F.346 Hydrogen bonds: D:Y.317

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.12: 3 residues within 4Å: Chain B: D.194, W.197, D.216 No protein-ligand interaction detected (PLIP) 1PE.21: 6 residues within 4Å: Chain C: E.177, R.178, P.200, N.227, Y.231, R.262 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.177, C:R.178, C:R.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weston, C.E. et al., Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors. ACS Infect Dis (2017)

Release Date

2016-11-23

Peptides

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE