SMTL ID : 5ojv.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-tetramer

Ligands

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: W.151, G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.2: 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.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: 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.5: 3 residues within 4Å: Chain A: Q.266, Y.286 Chain B: H.336 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: E.298, T.299, T.300, R.308, W.317 Ligand excluded by PLIP GOL.7: 10 residues within 4Å: Chain A: A.33, Y.38, W.42, W.44, D.45, Q.117, Q.436, W.438 Ligands: 2M8.8, SER.9 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: 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.13: 7 residues within 4Å: Chain C: W.151, G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.14: 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.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: 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.17: 3 residues within 4Å: Chain C: Q.266, Y.286 Chain D: H.336 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain C: E.298, T.299, T.300, R.308, W.317 Ligand excluded by PLIP GOL.19: 10 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, D.45, Q.117, Q.436, W.438 Ligands: 2M8.20, SER.21 Ligand excluded by PLIP GOL.22: 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.23: 7 residues within 4Å: Chain D: E.298, T.299, T.300, D.301, Q.302, R.308, W.317 Ligand excluded by PLIP

4 x 2M8: (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid(Non-covalent)

2M8.8: 17 residues within 4Å: Chain A: Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, G.182, D.184, R.218, Y.377, W.378, W.383, Q.436, W.438 Ligands: GOL.7, SER.9 12 PLIP interactions: 1 Ligand-Ligand interactions, 11 interactions with chain A Hydrogen bonds: S.9, A:Y.38, A:W.44, A:D.45, A:Q.117, A:G.182, A:Y.224, A:Y.377, A:Q.436 Water bridges: A:Y.90, A:R.218 Salt bridges: A:R.218 2M8.12: 18 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, W.383, Q.436, W.438 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:W.44, B:D.45, B:H.80, B:Y.90, B:Y.90, B:Q.117, B:G.182, B:D.184, B:Y.224, B:Y.377, B:Q.436 Water bridges: B:R.218 Salt bridges: B:R.218 2M8.20: 17 residues within 4Å: Chain C: Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, G.182, D.184, R.218, Y.377, W.378, W.383, Q.436, W.438 Ligands: GOL.19, SER.21 12 PLIP interactions: 11 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:Y.38, C:W.44, C:D.45, C:Q.117, C:G.182, C:Y.224, C:Y.377, C:Q.436, S.21 Water bridges: C:Y.90, C:R.218 Salt bridges: C:R.218 2M8.24: 18 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, W.383, Q.436, W.438 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:W.44, D:D.45, D:H.80, D:Y.90, D:Y.90, D:Q.117, D:G.182, D:D.184, D:Y.224, D:Y.377, D:Q.436 Water bridges: D:R.218 Salt bridges: D:R.218

2 x SER: SERINE(Non-covalent)

SER.9: 10 residues within 4Å: Chain A: Y.38, W.42, H.80, Y.90, D.184, R.218, Y.224, Y.377 Ligands: GOL.7, 2M8.8 10 PLIP interactions: 1 Ligand-Ligand interactions, 9 interactions with chain A Water bridges: S.9, A:Y.90, A:R.218, A:R.218, A:R.218 Hydrogen bonds: A:Y.38, A:Y.224, A:Y.377, A:Y.377 Salt bridges: A:R.218 SER.21: 10 residues within 4Å: Chain C: Y.38, W.42, H.80, Y.90, D.184, R.218, Y.224, Y.377 Ligands: GOL.19, 2M8.20 10 PLIP interactions: 9 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:Y.38, C:Y.224, C:Y.377, C:Y.377 Water bridges: C:Y.90, C:R.218, C:R.218, C:R.218, S.21 Salt bridges: C:R.218

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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