SMTL ID : 5oie.1

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) E419A variant in complex with serine and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Y.38, W.42, W.44, D.45, Q.117, Q.436, W.438 Ligands: SER.7 Ligand excluded by PLIP GOL.2: 6 residues within 4Å: Chain A: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: E.401, R.404 Chain B: R.127, H.131 Chain D: Q.13 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: E.298, T.299, T.300, D.301, R.308, W.317 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: Q.266, Y.286 Chain B: H.336 Ligand excluded by PLIP GOL.6: 2 residues within 4Å: Chain A: H.336 Chain B: Y.286 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain B: Y.38, W.42, W.44, D.45, Q.117, Q.436, W.438 Ligands: SER.13 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain B: W.151, G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: R.127, E.130, H.131 Chain B: E.401, R.404 Chain C: Q.13 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain B: E.298, T.299, T.300, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain C: Y.38, W.42, W.44, D.45, Q.117, Q.436, W.438 Ligands: SER.20 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain C: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: Q.13 Chain C: E.401, R.404 Chain D: R.127, H.131 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain C: E.298, T.299, T.300, D.301, R.308, W.317 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain C: Q.266, Y.286 Chain D: H.336 Ligand excluded by PLIP GOL.19: 2 residues within 4Å: Chain C: H.336 Chain D: Y.286 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain D: Y.38, W.42, W.44, D.45, Q.117, Q.436, W.438 Ligands: SER.26 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain D: W.151, G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain A: Q.13 Chain C: R.127, E.130, H.131 Chain D: E.401, R.404 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain D: E.298, T.299, T.300, Q.302, R.308, W.317 Ligand excluded by PLIP

4 x SER: SERINE(Non-covalent)

SER.7: 9 residues within 4Å: Chain A: Y.38, W.42, H.80, Y.90, D.184, R.218, Y.224, Y.377 Ligands: GOL.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.38, A:H.80, A:Y.224, A:Y.377, A:Y.377, A:Y.377 Water bridges: A:Y.90, A:Q.117, A:R.218, A:R.218 Salt bridges: A:R.218 SER.13: 9 residues within 4Å: Chain B: Y.38, W.42, H.80, Y.90, D.184, R.218, Y.224, Y.377 Ligands: GOL.9 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:H.80, B:Y.90, B:Y.90, B:D.184, B:Y.224, B:Y.377, S.13 Salt bridges: B:R.218 SER.20: 9 residues within 4Å: Chain C: Y.38, W.42, H.80, Y.90, D.184, R.218, Y.224, Y.377 Ligands: GOL.14 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.38, C:H.80, C:Y.224, C:Y.377, C:Y.377, C:Y.377 Water bridges: C:Y.90, C:Q.117, C:R.218, C:R.218 Salt bridges: C:R.218 SER.26: 9 residues within 4Å: Chain D: Y.38, W.42, H.80, Y.90, D.184, R.218, Y.224, Y.377 Ligands: GOL.22 8 PLIP interactions: 7 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:H.80, D:Y.90, D:Y.90, D:D.184, D:Y.224, D:Y.377, S.26 Salt bridges: D:R.218

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

PEG.8: 5 residues within 4Å: Chain A: Y.204, Q.205, R.206, N.209, D.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.206, A:N.209 PEG.21: 5 residues within 4Å: Chain C: Y.204, Q.205, R.206, N.209, D.221 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.206, C:N.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cereija, T.B. et al., The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation. Iucrj (2019)

Release Date

2018-08-08

Peptides

hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

hydrolase

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