SMTL ID : 8u01.1

Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domain Containing Protein from Phocaeicola plebeius

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: A.726, L.731, K.887 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: D.830, K.831 Ligand excluded by PLIP

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

SO4.3: 5 residues within 4Å: Chain A: P.719, A.721, R.880, Q.881, Y.884 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.881 Water bridges: A:R.880 SO4.4: 6 residues within 4Å: Chain A: K.661, E.662, P.697, S.698, C.699, P.805 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.661, A:C.699, A:C.699 Salt bridges: A:K.661

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 2 residues within 4Å: Chain A: D.487 Ligands: PEG.40 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.485, A:R.485 Salt bridges: A:R.485 ACT.18: 5 residues within 4Å: Chain A: N.454, L.455, P.456, Q.499 Ligands: PEG.12 No protein-ligand interaction detected (PLIP) ACT.21: 1 residues within 4Å: Chain A: W.452 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: W.378, E.420, W.471, E.505, Q.508, L.580, Q.588, F.776, W.777 Ligands: TAG.39 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.508, A:Q.588, A:Q.588 Water bridges: A:R.467, A:E.505 GOL.7: 9 residues within 4Å: Chain A: G.301, K.302, I.494, F.497, Q.498, Q.499, P.500, K.572, D.573 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.498 GOL.8: 3 residues within 4Å: Chain A: W.396, N.432, T.436 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.432, A:T.436, A:T.436 GOL.36: 4 residues within 4Å: Chain A: K.7, D.9, D.184, F.186 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.7, A:K.7 Water bridges: A:K.7, A:D.9, A:D.9

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 2 residues within 4Å: Chain A: H.673, Q.674 No protein-ligand interaction detected (PLIP) PEG.10: 4 residues within 4Å: Chain A: S.20, W.23, M.151 Ligands: EDO.17 No protein-ligand interaction detected (PLIP) PEG.11: 3 residues within 4Å: Chain A: S.548, C.794, Y.808 No protein-ligand interaction detected (PLIP) PEG.12: 3 residues within 4Å: Chain A: R.496, Q.498 Ligands: ACT.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.496 Water bridges: A:Q.498, A:Q.498 PEG.19: 1 residues within 4Å: Chain A: D.522 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.522 PEG.20: 6 residues within 4Å: Chain A: V.475, N.480, A.481, K.757, S.819, H.820 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.757, A:K.757, A:Q.871 PEG.27: 5 residues within 4Å: Chain A: N.380, Q.381, S.382, T.383, A.422 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.382 PEG.38: 3 residues within 4Å: Chain A: K.562, S.712, H.714 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.558, A:S.712 Water bridges: A:R.613 PEG.40: 5 residues within 4Å: Chain A: I.478, D.487, Y.488, D.489 Ligands: ACT.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.485

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

EDO.13: 4 residues within 4Å: Chain A: E.264, R.342, R.612, N.616 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: E.602, K.603 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: D.54, S.55, S.56, K.60 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: W.114, E.115, N.129, V.158, K.159, N.160, I.161 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: W.23, Q.91 Ligands: PEG.10 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: T.782, L.783 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain A: S.268, L.269 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: T.5, S.99 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: N.465, W.490, Y.493 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: L.793, P.835, R.838 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: E.332, K.335, K.336, T.339 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain A: P.30, S.35, N.36 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: Y.521, D.522, R.526 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain A: Q.632, A.720 Ligand excluded by PLIP EDO.32: 1 residues within 4Å: Chain A: D.330 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: D.162, S.382, T.383 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: P.267, G.366, M.367 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain A: H.820, K.875 Ligand excluded by PLIP

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

MES.37: 6 residues within 4Å: Chain A: M.201, E.203, S.210, D.441, A.442, R.443 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.441, A:A.442 Salt bridges: A:E.203

1 x TAG: D-tagatose(Non-covalent)

TAG.39: 5 residues within 4Å: Chain A: V.53, E.420, W.471, W.781 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.420, A:W.781 Water bridges: A:N.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domainContaining Protein from Phocaeicola plebeius. To Be Published

Release Date

2023-09-27

Peptides

Glycosyl hydrolase family 2, sugar binding domain protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycosyl hydrolase family 2, sugar binding domain protein