SMTL ID : 2wag.1

The Structure of a family 25 Glycosyl hydrolase from Bacillus anthracis.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

10 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.1: 8 residues within 4Å: Chain A: M.11, Y.14, P.172, S.173, K.179, W.180, Y.207 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.14 15P.9: 5 residues within 4Å: Chain A: F.78, D.79, S.80, K.81, D.121 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.121, A:E.125 15P.10: 5 residues within 4Å: Chain A: I.90, R.91, N.92, V.93, P.94 No protein-ligand interaction detected (PLIP) 15P.11: 3 residues within 4Å: Chain A: K.118, R.119, E.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.119, A:E.120, A:E.120 Water bridges: A:K.118 15P.12: 4 residues within 4Å: Chain A: Y.207, E.212, Y.216 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.212 Hydrogen bonds: A:Y.207 15P.14: 8 residues within 4Å: Chain B: M.11, Y.14, P.172, S.173, K.179, W.180, Y.207 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.14 15P.22: 5 residues within 4Å: Chain B: F.78, D.79, S.80, K.81, D.121 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.121 15P.23: 5 residues within 4Å: Chain B: I.90, R.91, N.92, V.93, P.94 No protein-ligand interaction detected (PLIP) 15P.24: 3 residues within 4Å: Chain B: K.118, R.119, E.120 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.119, B:E.120 Water bridges: B:K.118 15P.25: 4 residues within 4Å: Chain B: Y.207, E.212, Y.216 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.212

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: G.2, S.3, N.187, R.188, Y.200 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.3, A:N.187, A:Y.200 Water bridges: A:S.4, A:R.188, A:R.188 Salt bridges: A:R.188 SO4.3: 6 residues within 4Å: Chain A: H.9, H.10, K.17, Y.185, K.190, L.203 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.10, A:Y.185 Water bridges: A:K.17, A:K.17, A:K.17 Salt bridges: A:H.9, A:H.10, A:K.17, A:K.190 SO4.4: 3 residues within 4Å: Chain A: M.11, D.12, R.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.12, A:R.13 Salt bridges: A:R.13 SO4.5: 4 residues within 4Å: Chain A: R.166, S.167, V.168, L.169 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.166, A:V.168 Water bridges: A:Q.147, A:Q.147, A:R.166, A:R.166, A:R.166, A:L.169, A:L.169 Salt bridges: A:R.166 SO4.6: 5 residues within 4Å: Chain A: G.48, S.49, S.77, D.79, S.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.49, A:S.77, A:S.80 Water bridges: A:A.50 SO4.15: 5 residues within 4Å: Chain B: G.2, S.3, N.187, R.188, Y.200 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.3, B:N.187 Water bridges: B:S.4, B:R.188, B:R.188 Salt bridges: B:R.188 SO4.16: 6 residues within 4Å: Chain B: H.9, H.10, K.17, Y.185, K.190, L.203 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.10, B:Y.185, B:Y.185 Water bridges: B:K.17, B:K.17, B:K.17 Salt bridges: B:H.9, B:H.10, B:K.17, B:K.190 SO4.17: 3 residues within 4Å: Chain B: M.11, D.12, R.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.12, B:R.13 Salt bridges: B:R.13 SO4.18: 4 residues within 4Å: Chain B: R.166, S.167, V.168, L.169 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.166, B:V.168 Water bridges: B:Q.147, B:Q.147, B:R.166, B:R.166, B:R.166, B:L.169, B:L.169 Salt bridges: B:R.166 SO4.19: 5 residues within 4Å: Chain B: G.48, S.49, S.77, D.79, S.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.49, B:S.77, B:S.80 Water bridges: B:A.50

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: D.27, I.28, D.29, E.32, L.33, Q.36, L.191, S.192, N.195 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.27, A:D.29, A:Q.36, A:S.192 Water bridges: A:E.32, A:E.32 GOL.8: 7 residues within 4Å: Chain A: D.162, K.179, W.180, T.181, Y.207 Ligands: 15P.1, 15P.12 6 PLIP interactions: 6 interactions with chain A Water bridges: A:D.162, A:D.162, A:D.162, A:D.162, A:R.178, A:K.179 GOL.20: 9 residues within 4Å: Chain B: D.27, I.28, D.29, E.32, L.33, Q.36, L.191, S.192, N.195 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.27, B:D.29, B:Q.36, B:S.192 Water bridges: B:E.32, B:Y.194, B:N.195 GOL.21: 7 residues within 4Å: Chain B: D.162, K.179, W.180, T.181, Y.207 Ligands: 15P.14, 15P.25 6 PLIP interactions: 6 interactions with chain B Water bridges: B:D.162, B:D.162, B:D.162, B:R.178, B:K.179, B:T.181

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 7 residues within 4Å: Chain A: Y.150, I.154, K.155, D.156, A.157, D.176, R.178 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.154, A:A.157 MG.26: 7 residues within 4Å: Chain B: Y.150, I.154, K.155, D.156, A.157, D.176, R.178 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:I.154, B:A.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Fleites, C. et al., The Crystal Structure of a Family Gh25 Lysozyme from Bacillus Anthracis Implies a Neighboring-Group Catalytic Mechanism with Retention of Anomeric Configuration. Carbohydr.Res. (2009)

Release Date

2009-06-23

Peptides

LYSOZYME, PUTATIVE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LYSOZYME, PUTATIVE