SMTL ID : 5oi1.1

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with serine and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

22 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.9 Ligand excluded by PLIP GOL.2: 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.3: 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.4: 6 residues within 4Å: Chain A: G.152, M.155, R.156, R.159, P.278, D.281 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: 7 residues within 4Å: Chain A: E.298, T.299, T.300, D.301, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: Q.266, Y.286 Chain B: H.336 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: H.336 Chain B: Q.266, Y.286 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain B: Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: SER.13 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain B: G.152, M.155, R.156, R.159, P.278, D.281 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: 9 residues within 4Å: Chain C: Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: SER.22 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 A: Q.13 Chain C: R.127, E.130, H.131 Chain D: E.401, R.404 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain C: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.18: 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.19: 7 residues within 4Å: Chain C: E.298, T.299, T.300, D.301, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain C: Q.266, Y.286 Chain D: H.336 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain C: H.336 Chain D: Q.266, Y.286 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain D: Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: SER.26 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain D: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.25: 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 SER: SERINE(Non-covalent)

SER.9: 10 residues within 4Å: Chain A: Y.38, W.42, H.80, Y.90, Q.117, W.179, R.218, Y.224, Y.377 Ligands: GOL.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.90, A:Y.90, A:Q.117, A:R.218, A:Y.224, A:Y.224, A:Y.377 Salt bridges: A:H.80 SER.13: 9 residues within 4Å: Chain B: Y.38, W.42, H.80, Y.90, W.179, R.218, Y.224, Y.377 Ligands: GOL.10 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:R.218, B:R.218, B:Y.224, B:Y.377, B:Y.377, S.13, S.13 Water bridges: B:Y.90 Salt bridges: B:H.80 SER.22: 10 residues within 4Å: Chain C: Y.38, W.42, H.80, Y.90, Q.117, W.179, R.218, Y.224, Y.377 Ligands: GOL.14 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.90, C:Y.90, C:Q.117, C:R.218, C:Y.224, C:Y.224, C:Y.377 Salt bridges: C:H.80 SER.26: 9 residues within 4Å: Chain D: Y.38, W.42, H.80, Y.90, W.179, R.218, Y.224, Y.377 Ligands: GOL.23 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:R.218, D:R.218, D:Y.224, D:Y.377, D:Y.377, S.26, S.26 Water bridges: D:Y.90 Salt bridges: D:H.80

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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