SMTL ID : 5oju.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-tetramer

Ligands

4 x 9WN: (2R)-2-(alpha-D-glucopyranosyloxy)-3-hydroxypropanoic acid(Non-covalent)

9WN.1: 15 residues within 4Å: Chain A: A.33, Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, G.182, D.184, R.218, Y.377, W.378, Q.436, W.438 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.38, A:W.44, A:D.45, A:H.80, A:Q.117, A:G.182, A:Y.224, A:Y.377, A:Y.377, A:Q.436 Water bridges: A:Y.90, A:G.182, A:G.182, A:R.218 Salt bridges: A:R.218 9WN.9: 17 residues within 4Å: Chain B: A.33, Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, W.179, G.182, D.184, R.218, Y.224, Y.377, W.378, Q.436, W.438 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:W.44, B:D.45, B:D.45, B:H.80, B:Y.90, B:Y.90, B:Q.117, B:G.182, B:Q.436 Water bridges: B:Y.38, B:Y.38 Salt bridges: B:R.218 9WN.13: 15 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, G.182, D.184, R.218, Y.377, W.378, Q.436, W.438 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Y.38, C:W.44, C:D.45, C:H.80, C:Q.117, C:G.182, C:Y.224, C:Y.377, C:Y.377, C:Q.436 Water bridges: C:Y.90, C:G.182, C:G.182, C:R.218 Salt bridges: C:R.218 9WN.21: 17 residues within 4Å: Chain D: A.33, Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, W.179, G.182, D.184, R.218, Y.224, Y.377, W.378, Q.436, W.438 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:W.44, D:D.45, D:D.45, D:H.80, D:Y.90, D:Y.90, D:Q.117, D:G.182, D:Q.436 Water bridges: D:Y.38, D:Y.38 Salt bridges: D:R.218

18 x GOL: GLYCEROL(Non-functional Binders)

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: 6 residues within 4Å: Chain A: E.401, R.404 Chain B: R.127, E.130, 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: 7 residues within 4Å: Chain A: L.27, G.28, T.29, M.30, A.84, N.85, R.110 Ligand excluded by PLIP GOL.6: 2 residues within 4Å: Chain A: Q.266, Y.286 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: H.336 Chain B: Q.266, Y.286 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain B: G.152, M.155, R.156, R.159, 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: 7 residues within 4Å: Chain B: E.298, T.299, T.300, D.301, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain C: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: Q.13 Chain C: E.401, R.404 Chain D: R.127, E.130, H.131 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain C: E.298, T.299, T.300, D.301, R.308, W.317 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain C: L.27, G.28, T.29, M.30, A.84, N.85, R.110 Ligand excluded by PLIP GOL.18: 2 residues within 4Å: Chain C: Q.266, Y.286 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain C: H.336 Chain D: Q.266, Y.286 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain D: G.152, M.155, R.156, R.159, D.281 Ligand excluded by PLIP GOL.23: 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.24: 7 residues within 4Å: Chain D: E.298, T.299, T.300, D.301, Q.302, R.308, W.317 Ligand excluded by PLIP

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

PEG.8: 6 residues within 4Å: Chain A: Y.204, Q.205, R.206, N.209, D.221, D.225 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.206, A:N.209 Water bridges: A:Y.204, A:Q.205, A:Q.205, A:D.221, A:D.221 PEG.20: 6 residues within 4Å: Chain C: Y.204, Q.205, R.206, N.209, D.221, D.225 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.206, C:N.209 Water bridges: C:Y.204, C:Q.205, C:Q.205, C:D.221, C:D.221

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

Uncharacterized protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Uncharacterized protein

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