SMTL ID : 5oj4.1

Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with mannosylglycerate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-tetramer

Ligands

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: E.401, R.404 Chain B: R.127, E.130, H.131, G.448 Chain D: Q.13 Ligand excluded by PLIP GOL.2: 7 residues within 4Å: Chain A: R.127, E.130, H.131, G.448 Chain B: E.401, R.404 Chain C: 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: 6 residues within 4Å: Chain A: E.298, T.299, T.300, D.301, R.308, W.317 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: E.270, R.396 Chain B: R.397 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: 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.8: 5 residues within 4Å: Chain A: L.36, I.212, G.432, S.433, M.434 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain B: E.298, T.299, T.300, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain B: L.27, G.28, T.29, M.30, A.84, N.85, R.110 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain A: H.336 Chain B: Q.266, Y.286 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: I.211, G.432, S.433, M.434 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: R.170, R.172, E.298, F.310, W.317 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: S.246, V.247, M.248, S.249, L.313 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: Q.13 Chain C: E.401, R.404 Chain D: R.127, E.130, H.131, G.448 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain A: Q.13 Chain C: R.127, E.130, H.131, G.448 Chain D: E.401, R.404 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain C: G.152, M.155, R.156, R.159, P.278, D.281 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.27: 3 residues within 4Å: Chain C: E.270, R.396 Chain D: R.397 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain C: Q.266, Y.286 Chain D: H.336 Ligand excluded by PLIP GOL.29: 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.30: 5 residues within 4Å: Chain C: L.36, I.212, G.432, S.433, M.434 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain D: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain D: E.298, T.299, T.300, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain D: L.27, G.28, T.29, M.30, A.84, N.85, R.110 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain C: H.336 Chain D: Q.266, Y.286 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain D: I.211, G.432, S.433, M.434 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain D: R.170, R.172, E.298, F.310, W.317 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain D: S.246, V.247, M.248, S.249, L.313 Ligand excluded by PLIP

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

PEG.9: 5 residues within 4Å: Chain A: Y.204, Q.205, R.206, D.221, D.225 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.204, A:Q.205, A:R.206, A:D.225 Water bridges: A:R.206, A:N.209, A:N.209, A:D.221 PEG.10: 3 residues within 4Å: Chain A: R.133, D.274, Y.275 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.274, B:E.347 PEG.11: 6 residues within 4Å: Chain A: L.69, S.70, Q.72, R.150, D.153, R.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.72, A:R.150, A:R.150, A:R.156 PEG.31: 5 residues within 4Å: Chain C: Y.204, Q.205, R.206, D.221, D.225 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.204, C:Q.205, C:R.206, C:D.225 Water bridges: C:R.206, C:N.209, C:N.209, C:D.221 PEG.32: 3 residues within 4Å: Chain C: R.133, D.274, Y.275 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:D.274, D:E.347 PEG.33: 6 residues within 4Å: Chain C: L.69, S.70, Q.72, R.150, D.153, R.156 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.72, C:R.150, C:R.150, C:R.156

4 x GLY: GLYCINE(Non-covalent)

GLY.12: 5 residues within 4Å: Chain A: R.340, K.344, E.347, R.402 Chain B: D.274 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.402 Water bridges: A:R.340 Salt bridges: A:R.340, A:R.402 GLY.13: 3 residues within 4Å: Chain A: D.88, G.89, Y.90 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.88, A:G.89, A:Y.90, G.13, G.13 Water bridges: A:G.93 GLY.34: 5 residues within 4Å: Chain C: R.340, K.344, E.347, R.402 Chain D: D.274 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.402 Water bridges: C:R.340 Salt bridges: C:R.340, C:R.402 GLY.35: 3 residues within 4Å: Chain C: D.88, G.89, Y.90 6 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain C Hydrogen bonds: G.35, G.35, C:D.88, C:G.89, C:Y.90 Water bridges: C:G.93

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

2M8.14: 16 residues within 4Å: Chain A: A.33, Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, W.179, G.182, R.218, Y.377, W.378, W.383, Q.436, W.438 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.38, A:W.44, A:H.80, A:Q.117, A:G.182, A:Y.377, A:Y.377, A:Q.436 Water bridges: A:Y.90, A:Y.224, A:Y.377, A:Y.377, A:Y.377 Salt bridges: A:R.218 2M8.22: 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, R.218, Y.377, W.378, W.383, E.421, Q.436, W.438 16 PLIP interactions: 16 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:Y.377, B:Y.377, B:Q.436 Water bridges: B:Y.38, B:Y.38, B:G.182, B:R.218, B:R.218 Salt bridges: B:R.218 2M8.36: 16 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, W.179, G.182, R.218, Y.377, W.378, W.383, Q.436, W.438 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Y.38, C:W.44, C:H.80, C:Q.117, C:G.182, C:Y.377, C:Y.377, C:Q.436 Water bridges: C:Y.90, C:Y.224, C:Y.377, C:Y.377, C:Y.377 Salt bridges: C:R.218 2M8.44: 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, R.218, Y.377, W.378, W.383, E.421, Q.436, W.438 16 PLIP interactions: 16 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:Y.377, D:Y.377, D:Q.436 Water bridges: D:Y.38, D:Y.38, D:G.182, D:R.218, D:R.218 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
A

D
B

Hydrolase

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