SMTL ID : 2ww2.1

Structure of the Family GH92 Inverting Mannosidase BT2199 from Bacteroides thetaiotaomicron VPI-5482

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 6 residues within 4Å: Chain A: N.12, L.14, Y.56, G.618, S.619 Ligands: NA.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.14, A:Y.56 Hydrogen bonds: A:Y.56, A:Y.56, A:S.619 Water bridges: A:S.619

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: H.102, E.105 Ligands: MPD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.102, A:E.105 NA.3: 5 residues within 4Å: Chain A: S.19, Y.622, C.623, G.624, D.627 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.624, A:D.627 NA.11: 2 residues within 4Å: Chain B: H.102, E.105 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.105, B:E.105 Water bridges: B:K.106 NA.17: 2 residues within 4Å: Chain C: H.102, E.105 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.105, C:E.105

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: G.278, G.279, T.280, Q.283, R.608, L.658, K.660, N.679, A.680 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.280, A:Q.283, A:Q.283, A:R.608, A:N.679 Water bridges: A:R.608 GOL.5: 7 residues within 4Å: Chain A: P.13, N.27, Y.29, Y.292, R.293, L.296, F.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.13, A:Y.29, A:R.293 Water bridges: A:R.293 GOL.6: 8 residues within 4Å: Chain A: G.49, S.50, G.51, W.52, P.72, W.73, N.75 Chain B: E.541 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.51, A:W.52, A:N.75, B:E.541 Water bridges: A:P.72, B:E.541 GOL.7: 7 residues within 4Å: Chain A: H.25, P.70, S.71, D.333, W.370, Q.630 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.25 Water bridges: A:G.629, A:Q.630, A:Q.630 GOL.8: 8 residues within 4Å: Chain A: P.70, F.297, D.328, N.329, G.330, T.334, W.370 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.328, A:G.330, A:G.330 GOL.9: 3 residues within 4Å: Chain A: R.163, S.189, R.232 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.163, A:R.232, A:R.232 GOL.10: 4 residues within 4Å: Chain A: H.375, R.376, G.377, I.419 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.375, A:R.376, A:G.377 Water bridges: A:G.175, A:R.376, A:R.376, A:R.376 GOL.12: 7 residues within 4Å: Chain B: G.278, G.279, Q.283, R.608, L.658, K.660, A.680 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.280, B:Q.283, B:Q.283, B:R.608, B:K.660, B:K.660 Water bridges: B:R.608 GOL.13: 5 residues within 4Å: Chain B: R.163, E.187, F.188, S.189, R.232 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.163, B:R.163, B:E.187, B:R.232, B:R.232 GOL.14: 4 residues within 4Å: Chain B: A.581, H.582, C.623, G.624 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.582 GOL.15: 7 residues within 4Å: Chain B: V.34, P.35, W.36, S.128, Q.266, Y.270, E.300 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.128, B:E.300 Water bridges: B:S.128, B:R.352 GOL.18: 9 residues within 4Å: Chain C: G.278, G.279, Q.283, R.608, L.658, K.660, N.679, A.680, A.681 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.280, C:Q.283, C:Q.283, C:R.608, C:N.679 Water bridges: C:R.608 GOL.19: 4 residues within 4Å: Chain C: S.71, W.73, I.74, M.379 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.71, C:S.71 GOL.20: 5 residues within 4Å: Chain C: T.334, V.338, N.628, G.629, Q.630 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.628 Water bridges: C:D.333

1 x SWA: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL(Non-covalent)

SWA.16: 8 residues within 4Å: Chain B: S.71, W.73, W.332, D.333, W.370, M.379, E.516, D.627 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.370 Hydrogen bonds: B:D.333, B:D.333, B:E.516 Salt bridges: B:D.333, B:E.516, B:D.627

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, Y. et al., Mechanistic Insights Into a Ca2+-Dependent Family of A-Mannosidases in a Human Gut Symbiont. Nat.Chem.Biol. (2010)

Release Date

2009-12-29

Peptides

ALPHA-1,2-MANNOSIDASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

ALPHA-1,2-MANNOSIDASE

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