SMTL ID : 5fqe.2 (1 other biounit)

The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: S.136, L.137, N.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.138 FMT.57: 1 residues within 4Å: Chain A: L.52 No protein-ligand interaction detected (PLIP)

60 x BR: BROMIDE ION(Non-covalent)(Non-functional Binders)

BR.2: 2 residues within 4Å: Chain A: Y.497, K.498 Ligand excluded by PLIP BR.3: 3 residues within 4Å: Chain A: G.357, F.359, N.360 Ligand excluded by PLIP BR.4: 2 residues within 4Å: Chain A: N.313, R.369 Ligand excluded by PLIP BR.5: 2 residues within 4Å: Chain A: P.79, K.141 Ligand excluded by PLIP BR.6: 3 residues within 4Å: Chain A: S.407, F.408, R.411 Ligand excluded by PLIP BR.7: 4 residues within 4Å: Chain A: N.197, Q.437, N.477, K.540 Ligand excluded by PLIP BR.8: 4 residues within 4Å: Chain A: Q.317, Y.318, E.326 Ligands: BR.22 Ligand excluded by PLIP BR.9: 3 residues within 4Å: Chain A: S.36, L.54 Ligands: BR.58 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain A: P.191, E.195, Y.541 Ligand excluded by PLIP BR.11: 2 residues within 4Å: Chain A: N.330, P.331 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain A: K.217, K.266 Ligands: BR.25 Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain A: M.371, L.409 Ligands: BR.62 Ligand excluded by PLIP BR.14: 4 residues within 4Å: Chain A: N.313, R.315, N.330 Ligands: BR.29 Ligand excluded by PLIP BR.15: 3 residues within 4Å: Chain A: I.103, I.105, S.134 Ligand excluded by PLIP BR.16: 2 residues within 4Å: Chain A: K.217, E.218 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain A: A.546, N.548 Ligands: BR.18 Ligand excluded by PLIP BR.18: 2 residues within 4Å: Chain A: L.549 Ligands: BR.17 Ligand excluded by PLIP BR.19: 4 residues within 4Å: Chain A: R.117, S.118, Y.499, W.500 Ligand excluded by PLIP BR.20: 3 residues within 4Å: Chain A: R.315, Q.317, E.327 Ligand excluded by PLIP BR.21: 2 residues within 4Å: Chain A: L.337, N.340 Ligand excluded by PLIP BR.22: 4 residues within 4Å: Chain A: K.266, W.267, Q.317 Ligands: BR.8 Ligand excluded by PLIP BR.23: 2 residues within 4Å: Chain A: S.552, N.555 Ligand excluded by PLIP BR.24: 1 residues within 4Å: Chain A: K.109 Ligand excluded by PLIP BR.25: 3 residues within 4Å: Chain A: P.262 Ligands: BR.12, BR.26 Ligand excluded by PLIP BR.26: 3 residues within 4Å: Chain A: P.262 Ligands: BR.25, BR.27 Ligand excluded by PLIP BR.27: 4 residues within 4Å: Chain A: H.250, S.260, P.262 Ligands: BR.26 Ligand excluded by PLIP BR.28: 3 residues within 4Å: Chain A: N.119, S.121, Y.570 Ligand excluded by PLIP BR.29: 4 residues within 4Å: Chain A: W.312, N.313, R.315 Ligands: BR.14 Ligand excluded by PLIP BR.30: 2 residues within 4Å: Chain A: K.269, I.329 Ligand excluded by PLIP BR.31: 3 residues within 4Å: Chain A: P.331, T.332, S.335 Ligand excluded by PLIP BR.32: 1 residues within 4Å: Chain A: N.555 Ligand excluded by PLIP BR.33: 2 residues within 4Å: Chain A: W.253, W.312 Ligand excluded by PLIP BR.34: 2 residues within 4Å: Chain A: S.586, N.589 Ligand excluded by PLIP BR.35: 2 residues within 4Å: Chain A: R.590, N.593 Ligand excluded by PLIP BR.36: 2 residues within 4Å: Chain A: N.593, G.594 Ligand excluded by PLIP BR.37: 1 residues within 4Å: Chain A: K.234 Ligand excluded by PLIP BR.38: 2 residues within 4Å: Chain A: T.519, F.520 Ligand excluded by PLIP BR.39: 2 residues within 4Å: Chain A: R.242, G.302 Ligand excluded by PLIP BR.40: 1 residues within 4Å: Chain A: K.224 Ligand excluded by PLIP BR.41: 1 residues within 4Å: Chain A: R.155 Ligand excluded by PLIP BR.42: 4 residues within 4Å: Chain A: K.104, N.133, S.134, K.518 Ligand excluded by PLIP BR.43: 4 residues within 4Å: Chain A: K.50, N.76, S.77, N.142 Ligand excluded by PLIP BR.44: 2 residues within 4Å: Chain A: W.74, N.76 Ligand excluded by PLIP BR.45: 3 residues within 4Å: Chain A: L.192, P.193, S.194 Ligand excluded by PLIP BR.46: 3 residues within 4Å: Chain A: M.239, I.533, N.537 Ligand excluded by PLIP BR.47: 4 residues within 4Å: Chain A: E.110, T.111, L.112, P.126 Ligand excluded by PLIP BR.48: 3 residues within 4Å: Chain A: H.424, K.561, R.562 Ligand excluded by PLIP BR.49: 5 residues within 4Å: Chain A: L.419, S.420, D.451, Y.452, K.565 Ligand excluded by PLIP BR.50: 2 residues within 4Å: Chain A: P.297, E.298 Ligand excluded by PLIP BR.51: 3 residues within 4Å: Chain A: T.29, E.172, E.174 Ligand excluded by PLIP BR.52: 2 residues within 4Å: Chain A: D.278, Y.279 Ligand excluded by PLIP BR.53: 2 residues within 4Å: Chain A: N.423, N.425 Ligand excluded by PLIP BR.54: 2 residues within 4Å: Chain A: M.543, K.550 Ligand excluded by PLIP BR.55: 1 residues within 4Å: Chain A: R.581 Ligand excluded by PLIP BR.58: 1 residues within 4Å: Ligands: BR.9 Ligand excluded by PLIP BR.59: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.61: 1 residues within 4Å: Chain A: L.380 Ligand excluded by PLIP BR.62: 1 residues within 4Å: Ligands: BR.13 Ligand excluded by PLIP BR.63: 1 residues within 4Å: Chain A: N.568 Ligand excluded by PLIP

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

MPD.56: 5 residues within 4Å: Chain A: W.203, Q.256, Y.446, L.480, W.482 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.203, A:L.480, A:W.482 Hydrogen bonds: A:Q.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noach, I. et al., The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium Perfringens. J.Mol.Biol. (2016)

Release Date

2016-03-30

Peptides

BETA-N-ACETYLGALACTOSAMINIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

BETA-N-ACETYLGALACTOSAMINIDASE

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