SMTL ID : 5oiv.1

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D43A variant in complex with serine and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-tetramer

Ligands

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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.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: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: A.33, Y.38, W.42, W.44, Q.117, Q.436, W.438 Ligands: SER.10 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: H.336 Chain B: Q.266, Y.286 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: Q.266, Y.286 Chain B: H.336 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: L.36, I.211, I.212, G.432, S.433, M.434 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: Y.204, Q.205, R.206, D.221, D.225 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: E.298, T.299, T.300, D.301, R.308, W.317 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: W.151, M.155, R.156, R.159, D.281 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain B: A.33, Y.38, W.42, W.44, Q.117, Q.436, W.438 Ligands: SER.17 Ligand excluded by PLIP GOL.16: 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.18: 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.19: 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.20: 6 residues within 4Å: Chain C: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, Q.117, Q.436, W.438 Ligands: SER.27 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain C: H.336 Chain D: Q.266, Y.286 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain C: Q.266, Y.286 Chain D: H.336 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain C: L.36, I.211, I.212, G.432, S.433, M.434 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain C: Y.204, Q.205, R.206, D.221, D.225 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain C: E.298, T.299, T.300, D.301, R.308, W.317 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain D: W.151, M.155, R.156, R.159, D.281 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain D: A.33, Y.38, W.42, W.44, Q.117, Q.436, W.438 Ligands: SER.34 Ligand excluded by PLIP GOL.33: 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.10: 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.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.80, A:Y.377, A:Y.377, A:Y.377 Water bridges: A:Y.90, A:Y.90, A:Q.117, A:Y.224, A:Y.224 Salt bridges: A:R.218 SER.17: 9 residues within 4Å: Chain B: Y.38, W.42, H.80, Y.90, D.184, R.218, Y.224, Y.377 Ligands: GOL.15 9 PLIP interactions: 8 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.17 Water bridges: B:Q.117 Salt bridges: B:R.218 SER.27: 10 residues within 4Å: Chain C: Y.38, W.42, H.80, Y.90, W.179, D.184, R.218, Y.224, Y.377 Ligands: GOL.21 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:H.80, C:Y.377, C:Y.377, C:Y.377 Water bridges: C:Y.90, C:Y.90, C:Q.117, C:Y.224, C:Y.224 Salt bridges: C:R.218 SER.34: 9 residues within 4Å: Chain D: Y.38, W.42, H.80, Y.90, D.184, R.218, Y.224, Y.377 Ligands: GOL.32 9 PLIP interactions: 8 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.34 Water bridges: D:Q.117 Salt bridges: D:R.218

6 x GLY: GLYCINE(Non-covalent)

GLY.11: 5 residues within 4Å: Chain A: L.346, E.347, R.402, L.405, L.406 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.352, A:C.352 GLY.12: 6 residues within 4Å: Chain A: R.340, L.343, K.344, E.347, R.402 Chain B: D.274 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.347, A:R.402 Water bridges: A:R.340, B:D.274 Salt bridges: A:R.340, A:R.402 GLY.13: 4 residues within 4Å: Chain A: R.170, E.298, F.310, W.317 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.298, A:W.317, G.13 Salt bridges: A:R.170 GLY.28: 5 residues within 4Å: Chain C: L.346, E.347, R.402, L.405, L.406 2 PLIP interactions: 2 interactions with chain C Water bridges: C:C.352, C:C.352 GLY.29: 6 residues within 4Å: Chain C: R.340, L.343, K.344, E.347, R.402 Chain D: D.274 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.347, C:R.402 Water bridges: C:R.340, D:D.274 Salt bridges: C:R.340, C:R.402 GLY.30: 4 residues within 4Å: Chain C: R.170, E.298, F.310, W.317 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain C Hydrogen bonds: G.30, C:E.298, C:W.317 Salt bridges: C:R.170

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