SMTL ID : 3k11.1

Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

57 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: P.29, K.33, T.98, I.411, N.415 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: Y.20, Q.21, G.22, T.23, G.309, E.310 Chain C: Y.389 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: D.258, H.259 Chain B: R.301 Ligands: EDO.7 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: F.241, D.294, Y.295, A.298 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: D.280, V.281, L.282, E.284 Ligands: EDO.12 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: R.297, G.343, W.344, I.345, D.346 Chain C: T.257 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: I.242, R.249, H.259, A.261 Ligands: EDO.3 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: Y.82, D.145, R.191, R.193, W.200, D.202, M.206 Ligands: EDO.29 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: H.14, D.423 Chain C: R.193, W.200, G.377, T.378, G.379 Ligands: EDO.48 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: H.314, N.320, D.321, S.322, L.324 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: D.321, Y.388, Y.389 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.222, P.283 Ligands: EDO.5 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: P.243, E.244, K.245, G.246, R.301, G.302 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: Y.323, L.324, V.392 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: L.159, K.160, D.161, E.162 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: K.54, D.68, K.130, T.131, D.132 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: T.104, Q.108, L.157 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: Q.17, Y.20, Y.24, M.421 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: G.363, K.364, N.366, E.372 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: P.29, K.33, T.98, I.411, N.415 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: Y.389 Chain B: Y.20, Q.21, G.22, T.23, G.309, E.310 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: D.258, H.259 Chain C: R.301 Ligands: EDO.27 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: F.241, D.294, Y.295, A.298 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: D.280, V.281, L.282, E.284 Ligands: EDO.32 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: T.257 Chain B: R.297, G.343, W.344, I.345, D.346 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: I.242, R.249, H.259, A.261 Ligands: EDO.23 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain B: Y.82, D.145, R.191, R.193, W.200, D.202, M.206 Ligands: EDO.49 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain A: R.193, W.200, G.377, T.378, G.379 Chain B: H.14, D.423 Ligands: EDO.8 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: H.314, N.320, D.321, S.322, L.324 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: D.321, Y.388, Y.389 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: K.222, P.283 Ligands: EDO.25 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain B: P.243, E.244, K.245, G.246, R.301, G.302 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: Y.323, L.324, V.392 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain B: L.159, K.160, D.161, E.162 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: K.54, D.68, K.130, T.131, D.132 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: T.104, Q.108, L.157 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: Q.17, Y.20, Y.24, M.421 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain B: G.363, K.364, N.366, E.372 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain C: P.29, K.33, T.98, I.411, N.415 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain B: Y.389 Chain C: Y.20, Q.21, G.22, T.23, G.309, E.310 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain A: R.301 Chain C: D.258, H.259 Ligands: EDO.47 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain C: F.241, D.294, Y.295, A.298 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain C: D.280, V.281, L.282, E.284 Ligands: EDO.52 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain B: T.257 Chain C: R.297, G.343, W.344, I.345, D.346 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain C: I.242, R.249, H.259, A.261 Ligands: EDO.43 Ligand excluded by PLIP EDO.48: 8 residues within 4Å: Chain C: Y.82, D.145, R.191, R.193, W.200, D.202, M.206 Ligands: EDO.9 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain B: R.193, W.200, G.377, T.378, G.379 Chain C: H.14, D.423 Ligands: EDO.28 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain C: H.314, N.320, D.321, S.322, L.324 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain C: D.321, Y.388, Y.389 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain C: K.222, P.283 Ligands: EDO.45 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain C: P.243, E.244, K.245, G.246, R.301, G.302 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain C: Y.323, L.324, V.392 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain C: L.159, K.160, D.161, E.162 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain C: K.54, D.68, K.130, T.131, D.132 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain C: T.104, Q.108, L.157 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain C: Q.17, Y.20, Y.24, M.421 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain C: G.363, K.364, N.366, E.372 Ligand excluded by PLIP

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.20: 6 residues within 4Å: Chain A: Q.433, K.434, T.435, F.440, A.441, D.443 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.434, A:A.441, A:A.441 Water bridges: A:A.441, A:V.442, A:D.443 Salt bridges: A:D.443 MES.40: 6 residues within 4Å: Chain B: Q.433, K.434, T.435, F.440, A.441, D.443 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.434, B:A.441, B:A.441 Water bridges: B:A.441, B:V.442, B:D.443 Salt bridges: B:D.443 MES.60: 6 residues within 4Å: Chain C: Q.433, K.434, T.435, F.440, A.441, D.443 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.434, C:A.441, C:A.441 Water bridges: C:A.441, C:V.442, C:D.443 Salt bridges: C:D.443

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. To be Published

Release Date

2009-11-03

Peptides

Putative glycosyl hydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Putative glycosyl hydrolase