SMTL ID : 5ohz.1

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) - SeMet derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-tetramer

Ligands

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: SER.5 Ligand excluded by PLIP GOL.2: 6 residues within 4Å: Chain A: E.298, T.299, T.300, R.308, W.317, V.319 Ligand excluded by PLIP GOL.3: 2 residues within 4Å: Chain A: H.336 Chain C: Y.286 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: R.127, W.388, S.391, W.392, D.445, W.446 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain B: Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: SER.12 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: Q.13 Chain B: R.127, E.130, H.131 Chain D: E.401, R.404 Ligand excluded by PLIP GOL.8: 2 residues within 4Å: Chain B: H.336 Chain D: Y.286 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain B: W.151, G.152, M.155, R.159, P.278, D.281 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain B: E.298, T.299, T.300, R.308, W.317 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain B: R.127, W.388, S.391, W.392, D.445, W.446 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: R.127, E.130, H.131, G.448 Chain B: Q.13 Chain C: E.401, R.404 Ligand excluded by PLIP GOL.14: 10 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: SER.17 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: E.401, R.404 Chain C: R.127, H.131, G.448 Chain D: Q.13 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.18: 10 residues within 4Å: Chain D: A.33, Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: SER.20 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: E.401, R.404 Chain C: Q.13 Chain D: R.127, E.130, H.131, D.445 Ligand excluded by PLIP

4 x SER: SERINE(Non-covalent)

SER.5: 10 residues within 4Å: Chain A: Y.38, W.42, H.80, Y.90, W.179, D.184, R.218, Y.224, Y.377 Ligands: GOL.1 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:H.80, A:Y.90, A:Y.90, A:Y.224, A:Y.377, S.5 Salt bridges: A:R.218 SER.12: 10 residues within 4Å: Chain B: Y.38, W.42, H.80, Y.90, W.179, D.184, R.218, Y.224, Y.377 Ligands: GOL.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.80, B:Y.90, B:Y.224, B:Y.377, B:Y.377 Water bridges: B:Y.90, B:Q.117, B:R.218, B:R.218 Salt bridges: B:R.218 SER.17: 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 10 PLIP interactions: 8 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:H.80, C:Y.90, C:Y.90, C:Y.224, C:Y.377, S.17 Water bridges: C:R.218, C:R.218, S.17 Salt bridges: C:R.218 SER.20: 10 residues within 4Å: Chain D: Y.38, W.42, H.80, Y.90, W.179, D.184, R.218, Y.224, Y.377 Ligands: GOL.18 11 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:Y.38, D:H.80, D:D.184, D:Y.224, D:Y.377, D:Y.377, D:Y.377 Water bridges: D:Y.90, D:R.218, S.20 Salt bridges: D: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

Hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hydrolase

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