SMTL ID : 5oo2.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-tetramer

Ligands

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.2: 3 residues within 4Å: Chain A: R.133, D.274, Y.275 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: E.298, T.299, T.300, R.308, W.317 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: L.346, E.347, G.360, R.402, L.405, L.406 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: 10 residues within 4Å: Chain A: A.33, Y.38, W.42, W.44, D.45, Q.117, Q.436, W.438 Ligands: 9YW.7, SER.8 Ligand excluded by PLIP GOL.9: 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.10: 6 residues within 4Å: Chain B: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.11: 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.12: 6 residues within 4Å: Chain B: E.298, T.299, T.300, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.13: 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.15: 6 residues within 4Å: Chain C: G.152, M.155, R.156, R.159, P.278, D.281 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain C: R.133, D.274, Y.275 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain C: E.298, T.299, T.300, R.308, W.317 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain C: L.346, E.347, G.360, R.402, L.405, L.406 Ligand excluded by PLIP GOL.19: 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.20: 10 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, D.45, Q.117, Q.436, W.438 Ligands: 9YW.21, SER.22 Ligand excluded by PLIP GOL.23: 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.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: 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.26: 6 residues within 4Å: Chain D: E.298, T.299, T.300, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain D: L.27, G.28, T.29, M.30, A.84, N.85, R.110 Ligand excluded by PLIP

4 x 9YW: (alpha-D-glucopyranosyloxy)acetic acid(Non-covalent)

9YW.7: 17 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, D.184, Y.377, W.378, Q.436, W.438 Ligands: GOL.6, SER.8 12 PLIP interactions: 8 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:W.44, A:D.45, A:Y.90, A:Q.117, A:Q.436, S.8, S.8, S.8 Water bridges: A:Q.436, A:Q.436, S.8 Salt bridges: A:H.80 9YW.14: 14 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, W.378, Q.436, W.438 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:W.44, B:D.45, B:Y.90, B:Q.117, B:G.182, B:Q.436 Water bridges: B:D.184, B:D.184 Salt bridges: B:H.80 9YW.21: 17 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, D.184, Y.377, W.378, Q.436, W.438 Ligands: GOL.20, SER.22 12 PLIP interactions: 8 interactions with chain C, 4 Ligand-Ligand interactions Hydrogen bonds: C:W.44, C:D.45, C:Y.90, C:Q.117, C:Q.436, S.22, S.22, S.22 Water bridges: C:Q.436, C:Q.436, S.22 Salt bridges: C:H.80 9YW.28: 14 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, W.378, Q.436, W.438 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:W.44, D:D.45, D:Y.90, D:Q.117, D:G.182, D:Q.436 Water bridges: D:D.184, D:D.184 Salt bridges: D:H.80

2 x SER: SERINE(Non-covalent)

SER.8: 11 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.6, 9YW.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.80, A:Y.90, A:Y.90, A:Y.224, A:Y.377 Water bridges: A:Q.117, A:D.184, A:D.184 Salt bridges: A:R.218 SER.22: 11 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.20, 9YW.21 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.80, C:Y.90, C:Y.90, C:Y.224, C:Y.377 Water bridges: C:Q.117, C:D.184, C:D.184 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

2018-08-29

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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