SMTL ID : 6tn6.1

X-ray structure of the endo-beta-1,4-mannanase from Thermotoga petrophila

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

MPD.1: 7 residues within 4Å: Chain A: Y.132, R.133, K.138, T.185, E.188, W.189, E.192 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.185, A:E.188 Hydrogen bonds: A:R.133, A:K.138 MPD.2: 1 residues within 4Å: Chain A: E.246 No protein-ligand interaction detected (PLIP) MPD.3: 2 residues within 4Å: Chain A: N.422, E.423 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.423 Hydrogen bonds: A:N.422

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

EDO.4: 6 residues within 4Å: Chain A: Y.21, Y.25, K.61, Y.343, Y.346 Ligands: CO3.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.61, A:Y.343 EDO.5: 7 residues within 4Å: Chain A: W.110, R.176, W.229, H.259, W.260 Ligands: EDO.6, EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.176, A:R.176, A:W.260 Water bridges: A:H.259 EDO.6: 3 residues within 4Å: Chain A: W.229, W.234 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: S.56, Y.57, R.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.56 Water bridges: A:D.111, A:R.121 EDO.9: 5 residues within 4Å: Chain A: W.110, D.112, E.174 Ligands: EDO.5, TRS.18 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain A: V.154, Y.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.155 EDO.14: 4 residues within 4Å: Chain A: I.331, R.340, G.341, Y.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.341 EDO.16: 5 residues within 4Å: Chain A: E.55, S.56, R.59, Y.64 Ligands: PEG.15 No protein-ligand interaction detected (PLIP) EDO.17: 6 residues within 4Å: Chain A: N.117, V.120, R.121, T.126, H.127, H.128 No protein-ligand interaction detected (PLIP)

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

ACT.8: 9 residues within 4Å: Chain A: K.11, E.12, F.13, F.15, L.205, F.250, P.288, V.290, D.321 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.13 Hydrogen bonds: A:D.321

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.10: 5 residues within 4Å: Chain A: D.112, F.113, W.326 Ligands: EDO.4, TRS.18 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.326 CO3.11: 3 residues within 4Å: Chain A: Q.82, E.86, R.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.87 Water bridges: A:E.86, A:E.86

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain A: Y.90, A.93, K.94, E.97, Y.155 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.93, A:E.97

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

PEG.15: 9 residues within 4Å: Chain A: E.55, Y.64, P.67, E.68, P.75, E.76, G.77, I.78 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.55 Water bridges: A:E.76

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.18: 14 residues within 4Å: Chain A: R.47, W.49, W.110, D.112, N.173, E.174, H.254, Y.256, H.259, E.293, W.326, F.349 Ligands: EDO.9, CO3.10 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.173, A:N.173, A:E.174, A:Y.256 Water bridges: A:W.110, A:D.112, A:H.259, A:W.326

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

CL.19: 4 residues within 4Å: Chain A: N.109, W.110, H.128, R.176 Ligand excluded by PLIP

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

NA.20: 5 residues within 4Å: Chain A: N.19, N.20, Y.21, W.326, M.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.19, A:Y.21 Water bridges: A:N.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

da Silva, V.M. et al., High-resolution structure of a modular hyperthermostable endo-beta-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain. Biochim Biophys Acta Proteins Proteom (2020)

Release Date

2020-04-29

Peptides

Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5