SMTL ID : 6qyh.1

Structure of Apo HPAB from E.coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: E.359 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.359, H2O.8, H2O.8, H2O.9, H2O.11, H2O.11 CA.11: 3 residues within 4Å: Chain B: E.394 Chain D: E.455 Ligands: CA.26 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: B:E.394, D:E.455, H2O.15, H2O.31, H2O.34 CA.12: 1 residues within 4Å: Chain B: G.26 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:G.26, H2O.11, H2O.13, H2O.15 CA.16: 1 residues within 4Å: Chain C: E.359 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.359, H2O.27, H2O.28, H2O.28, H2O.30, H2O.31 CA.26: 3 residues within 4Å: Chain B: E.455 Chain D: E.394 Ligands: CA.11 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: D:E.394, B:E.455, H2O.12, H2O.15, H2O.34 CA.27: 1 residues within 4Å: Chain D: G.26 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:G.26, H2O.30, H2O.33, H2O.34

8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 5 residues within 4Å: Chain A: R.105, D.314, R.346 Chain B: N.481, K.484 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.346, A:R.346 Water bridges: A:R.105, B:N.481 PGE.3: 8 residues within 4Å: Chain A: P.383, M.384, A.387, I.459, Q.465, R.469 Chain C: D.338, R.395 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.395, A:P.383, A:R.469 Water bridges: C:G.334, C:D.338, C:N.396, A:M.384, A:D.466 PGE.4: 3 residues within 4Å: Chain A: Q.65, N.71, Y.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.71 Water bridges: A:N.71 PGE.13: 6 residues within 4Å: Chain A: N.481, K.484, M.485 Chain B: R.105, D.314, R.346 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:N.481, B:R.105, B:R.105 Hydrogen bonds: B:R.346, B:R.346 PGE.17: 5 residues within 4Å: Chain C: R.105, D.314, R.346 Chain D: N.481, K.484 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Water bridges: D:N.481, C:R.105 Hydrogen bonds: C:R.346, C:R.346 PGE.18: 8 residues within 4Å: Chain A: D.338, R.395 Chain C: P.383, M.384, A.387, I.459, Q.465, R.469 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:P.383, C:R.469, A:R.395 Water bridges: C:M.384, C:D.466, A:G.334, A:D.338, A:N.396 PGE.19: 3 residues within 4Å: Chain C: Q.65, N.71, Y.79 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.71 Water bridges: C:N.71 PGE.28: 6 residues within 4Å: Chain C: N.481, K.484, M.485 Chain D: R.105, D.314, R.346 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.346, D:R.346 Water bridges: D:R.105, D:R.105, C:N.481

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

PEG.5: 5 residues within 4Å: Chain A: D.73, K.88, G.126, A.127, N.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.88, A:N.365 PEG.6: 9 residues within 4Å: Chain A: S.358, E.359 Chain B: A.90, D.91, R.94, R.97, D.354, C.357, S.358 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.97, B:D.354, A:E.359 PEG.7: 5 residues within 4Å: Chain A: L.178, E.179, E.181, D.219, R.283 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.181 PEG.8: 2 residues within 4Å: Chain A: D.91, Q.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.91 PEG.9: 4 residues within 4Å: Chain A: T.41 Chain B: D.511, I.512 Chain D: L.518 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.41, A:T.41 PEG.10: 4 residues within 4Å: Chain A: D.511, I.512 Chain B: T.41 Chain C: L.518 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.41 PEG.14: 6 residues within 4Å: Chain B: Q.54, D.57, A.58, K.61, M.64, L.106 No protein-ligand interaction detected (PLIP) PEG.20: 5 residues within 4Å: Chain C: D.73, K.88, G.126, A.127, N.365 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.88, C:N.365 PEG.21: 9 residues within 4Å: Chain C: S.358, E.359 Chain D: A.90, D.91, R.94, R.97, D.354, C.357, S.358 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.91, D:R.97, C:E.359 PEG.22: 5 residues within 4Å: Chain C: L.178, E.179, E.181, D.219, R.283 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.181 PEG.23: 2 residues within 4Å: Chain C: D.91, Q.95 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.91 PEG.24: 4 residues within 4Å: Chain B: L.518 Chain C: T.41 Chain D: D.511, I.512 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.41 PEG.25: 4 residues within 4Å: Chain A: L.518 Chain C: D.511, I.512 Chain D: T.41 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.41 PEG.29: 6 residues within 4Å: Chain D: Q.54, D.57, A.58, K.61, M.64, L.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.57

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.15: 5 residues within 4Å: Chain B: W.70, N.71, R.85, S.89, D.92 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.71, B:S.89, B:S.89 Water bridges: B:R.85 Salt bridges: B:D.92, B:D.92 pi-Cation interactions: B:W.70 EPE.30: 5 residues within 4Å: Chain D: W.70, N.71, R.85, S.89, D.92 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.71, D:S.89, D:S.89 Water bridges: D:R.85 Salt bridges: D:D.92, D:D.92 pi-Cation interactions: D:W.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, Y. et al., Structural and Functional Characterization of 4-Hydroxyphenylacetate 3-Hydroxylase from Escherichia coli. Chembiochem (2020)

Release Date

2019-06-12

Peptides

4-hydroxyphenylacetate 3-monooxygenase oxygenase component: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

4-hydroxyphenylacetate 3-monooxygenase oxygenase component

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