SMTL ID : 5onz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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.2: 5 residues within 4Å: Chain A: G.152, M.155, R.156, P.278, D.281 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: Y.204, Q.205, R.206, D.221, D.225 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: 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: 5 residues within 4Å: Chain A: E.169, R.170, R.291, A.294, G.295 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: 12 residues within 4Å: Chain A: A.33, Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: 9YW.9, 9YW.10, SER.11 Ligand excluded by PLIP GOL.12: 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.13: 4 residues within 4Å: Chain B: M.155, R.159, P.278, D.281 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain A: H.336 Chain B: Q.266, Y.286 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: E.298, T.299, T.300, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.16: 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.17: 6 residues within 4Å: Chain B: L.346, E.347, G.360, R.402, L.405, L.406 Ligand excluded by PLIP GOL.18: 10 residues within 4Å: Chain B: Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: 9YW.19, SER.20 Ligand excluded by PLIP GOL.21: 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.22: 5 residues within 4Å: Chain C: G.152, M.155, R.156, P.278, D.281 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain C: Y.204, Q.205, R.206, D.221, D.225 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain C: E.298, T.299, T.300, D.301, R.308, W.317 Ligand excluded by PLIP GOL.25: 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.26: 5 residues within 4Å: Chain C: E.169, R.170, R.291, A.294, G.295 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain C: Q.266, Y.286 Chain D: H.336 Ligand excluded by PLIP GOL.28: 12 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: 9YW.29, 9YW.30, SER.31 Ligand excluded by PLIP GOL.32: 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.33: 4 residues within 4Å: Chain D: M.155, R.159, P.278, D.281 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain C: H.336 Chain D: Q.266, Y.286 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain D: E.298, T.299, T.300, Q.302, R.308, W.317 Ligand excluded by PLIP GOL.36: 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.37: 6 residues within 4Å: Chain D: L.346, E.347, G.360, R.402, L.405, L.406 Ligand excluded by PLIP GOL.38: 10 residues within 4Å: Chain D: Y.38, W.42, W.44, D.45, Q.117, Y.377, Q.436, W.438 Ligands: 9YW.39, SER.40 Ligand excluded by PLIP

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

9YW.9: 16 residues within 4Å: Chain A: A.33, Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, G.182, Y.377, W.378, Q.436, W.438 Ligands: GOL.8, 9YW.10, SER.11 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: S.11, A:W.44, A:D.45, A:D.45, A:Q.117, A:Y.377, A:Q.436 Water bridges: A:Y.90 Salt bridges: A:H.80 9YW.10: 16 residues within 4Å: Chain A: A.33, Y.38, W.42, W.44, D.45, Y.90, Q.117, G.182, R.218, Y.377, W.378, Q.436, W.438 Ligands: GOL.8, 9YW.9, SER.11 15 PLIP interactions: 2 Ligand-Ligand interactions, 13 interactions with chain A Hydrogen bonds: S.11, A:Y.38, A:W.44, A:D.45, A:D.45, A:Q.117, A:G.182, A:Y.224, A:Y.377, A:Y.377, A:Q.436 Water bridges: S.11, A:G.182, A:R.218 Salt bridges: A:R.218 9YW.19: 16 residues within 4Å: Chain B: A.33, Y.38, W.42, W.44, D.45, Y.90, Q.117, G.182, R.218, Y.224, Y.377, W.378, Q.436, W.438 Ligands: GOL.18, SER.20 14 PLIP interactions: 11 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: B:W.44, B:D.45, B:D.45, B:Y.90, B:Y.90, B:Q.117, B:Y.377, B:Q.436, S.20, S.20 Water bridges: B:E.421, B:E.421, S.20 Salt bridges: B:R.218 9YW.29: 16 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, D.45, H.80, Y.90, Q.117, G.182, Y.377, W.378, Q.436, W.438 Ligands: GOL.28, 9YW.30, SER.31 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:W.44, C:D.45, C:D.45, C:Q.117, C:Y.377, C:Q.436, S.31 Water bridges: C:Y.90 Salt bridges: C:H.80 9YW.30: 16 residues within 4Å: Chain C: A.33, Y.38, W.42, W.44, D.45, Y.90, Q.117, G.182, R.218, Y.377, W.378, Q.436, W.438 Ligands: GOL.28, 9YW.29, SER.31 15 PLIP interactions: 13 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:Y.38, C:W.44, C:D.45, C:D.45, C:Q.117, C:G.182, C:Y.224, C:Y.377, C:Y.377, C:Q.436, S.31 Water bridges: C:G.182, C:R.218, S.31 Salt bridges: C:R.218 9YW.39: 16 residues within 4Å: Chain D: A.33, Y.38, W.42, W.44, D.45, Y.90, Q.117, G.182, R.218, Y.224, Y.377, W.378, Q.436, W.438 Ligands: GOL.38, SER.40 14 PLIP interactions: 11 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: D:W.44, D:D.45, D:D.45, D:Y.90, D:Y.90, D:Q.117, D:Y.377, D:Q.436, S.40, S.40 Water bridges: D:E.421, D:E.421, S.40 Salt bridges: D:R.218

4 x SER: SERINE(Non-covalent)

SER.11: 11 residues within 4Å: Chain A: Y.38, W.42, H.80, Y.90, W.179, R.218, Y.224, Y.377 Ligands: GOL.8, 9YW.9, 9YW.10 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.218, A:Y.224, A:Y.224, A:Y.377, A:Y.377 Water bridges: A:Y.90, A:Q.117 Salt bridges: A:H.80 SER.20: 9 residues within 4Å: Chain B: W.42, H.80, Y.90, W.179, R.218, Y.224, Y.377 Ligands: GOL.18, 9YW.19 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:Y.90, B:Y.90, B:R.218, B:Y.224, S.20 Water bridges: B:Q.117, B:Y.377, S.20 Salt bridges: B:H.80 SER.31: 11 residues within 4Å: Chain C: Y.38, W.42, H.80, Y.90, W.179, R.218, Y.224, Y.377 Ligands: GOL.28, 9YW.29, 9YW.30 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.218, C:Y.224, C:Y.224, C:Y.377, C:Y.377 Water bridges: C:Y.90, C:Q.117 Salt bridges: C:H.80 SER.40: 9 residues within 4Å: Chain D: W.42, H.80, Y.90, W.179, R.218, Y.224, Y.377 Ligands: GOL.38, 9YW.39 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:Y.90, D:Y.90, D:R.218, D:Y.224, S.40 Water bridges: D:Q.117, D:Y.377, S.40 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

2018-08-29

Peptides

Hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Hydrolase

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