SMTL ID : 5g1b.1

Bordetella Alcaligenes HDAH native

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.144, D.182, H.184, D.270 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.182, A:H.184, A:D.270, H2O.11, H2O.12 ZN.8: 3 residues within 4Å: Chain B: D.182, H.184, D.270 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.182, B:H.184, B:D.270, H2O.28, H2O.29 ZN.15: 4 residues within 4Å: Chain C: H.144, D.182, H.184, D.270 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.182, C:H.184, C:D.270, H2O.46, H2O.48 ZN.22: 3 residues within 4Å: Chain D: D.182, H.184, D.270 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.182, D:H.184, D:D.270, H2O.63, H2O.64

8 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.180, D.182, H.184, G.186, S.203, L.204 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.180, A:D.182, A:H.184, A:S.203, A:L.204 K.3: 5 residues within 4Å: Chain A: W.193, D.196, V.199, T.201, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.196, A:V.199, A:Y.228, H2O.13, H2O.13 K.9: 7 residues within 4Å: Chain B: D.180, D.182, H.184, G.186, S.203, L.204, H.205 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.180, B:D.182, B:H.184, B:S.203, B:L.204 K.10: 5 residues within 4Å: Chain B: W.193, D.196, V.199, T.201, Y.228 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.196, B:V.199, B:Y.228, H2O.29, H2O.29 K.16: 6 residues within 4Å: Chain C: D.180, D.182, H.184, G.186, S.203, L.204 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.180, C:D.182, C:H.184, C:S.203, C:L.204 K.17: 5 residues within 4Å: Chain C: W.193, D.196, V.199, T.201, Y.228 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.196, C:V.199, C:Y.228, H2O.48, H2O.48 K.23: 7 residues within 4Å: Chain D: D.180, D.182, H.184, G.186, S.203, L.204, H.205 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.180, D:D.182, D:H.184, D:S.203, D:L.204 K.24: 5 residues within 4Å: Chain D: W.193, D.196, V.199, T.201, Y.228 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.196, D:V.199, D:Y.228, H2O.64, H2O.65

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

1PE.4: 5 residues within 4Å: Chain A: E.174, R.175, P.197, N.224, Y.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.174, A:R.175 Water bridges: A:R.175 1PE.11: 5 residues within 4Å: Chain B: E.174, R.175, P.197, N.224, Y.228 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.224 Water bridges: B:Y.228 1PE.18: 5 residues within 4Å: Chain C: E.174, R.175, P.197, N.224, Y.228 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.174, C:R.175 Water bridges: C:R.175 1PE.25: 5 residues within 4Å: Chain D: E.174, R.175, P.197, N.224, Y.228 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.224 Water bridges: D:Y.228

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

PEG.5: 1 residues within 4Å: Chain A: R.357 No protein-ligand interaction detected (PLIP) PEG.6: 2 residues within 4Å: Chain A: P.63, A.65 No protein-ligand interaction detected (PLIP) PEG.7: 2 residues within 4Å: Chain A: D.285, H.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.341 PEG.12: 1 residues within 4Å: Chain B: R.357 No protein-ligand interaction detected (PLIP) PEG.13: 6 residues within 4Å: Chain B: Q.190, D.191, W.194, D.213, S.214, E.219 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.213 Water bridges: B:D.191, B:D.191 PEG.14: 2 residues within 4Å: Chain B: T.129, E.131 No protein-ligand interaction detected (PLIP) PEG.19: 1 residues within 4Å: Chain C: R.357 No protein-ligand interaction detected (PLIP) PEG.20: 2 residues within 4Å: Chain C: P.63, A.65 No protein-ligand interaction detected (PLIP) PEG.21: 2 residues within 4Å: Chain C: D.285, H.341 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.341 PEG.26: 1 residues within 4Å: Chain D: R.357 No protein-ligand interaction detected (PLIP) PEG.27: 6 residues within 4Å: Chain D: Q.190, D.191, W.194, D.213, S.214, E.219 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.213 Water bridges: D:D.191, D:D.191 PEG.28: 2 residues within 4Å: Chain D: T.129, E.131 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyners, C. et al., The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket. Biochim. Biophys. Acta (2017)

Release Date

2017-04-12

Peptides

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE

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