SMTL ID : 4y7e.3 (2 other biounits)

Crystal structure of beta-mannanase from Streptomyces thermolilacinus with mannohexaose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

1 x BMA- BMA- BMA- BMA- BMA- BMA- BMA: beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose

BMA-BMA-BMA-BMA-BMA-BMA-BMA.1: 25 residues within 4Å: Chain A: W.65, Y.66, W.94, H.121, N.162, E.163, N.167, N.199, W.200, Q.202, W.204, Y.231, V.233, W.266, W.288, G.292, N.293, T.294 Ligands: BMA.5, BMA.6, BMA.7, BMA.8, BMA.9, BMA.10, BMA.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.65

1 x BMA- BMA- BMA: beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose

BMA-BMA-BMA.2: 8 residues within 4Å: Chain B: W.65, Y.66, W.94, W.288, G.292, N.293, T.294 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.65

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.241, T.273, A.276, A.277, R.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.280 GOL.4: 7 residues within 4Å: Chain A: A.103, I.106, D.107, K.110, V.148, Q.152 Chain B: P.67 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.107, A:K.110, A:V.148, B:T.95, B:T.95 Water bridges: A:Q.152 GOL.14: 5 residues within 4Å: Chain B: D.241, T.273, A.276, A.277, R.280 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.280 GOL.15: 8 residues within 4Å: Chain B: V.41, Q.42, G.43, G.44, R.213, Y.216, G.251, L.252 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.43, B:G.44, B:R.213, B:R.213 Water bridges: B:G.43, B:G.251 GOL.16: 3 residues within 4Å: Chain A: K.335 Chain B: D.140, I.143 No protein-ligand interaction detected (PLIP) GOL.17: 5 residues within 4Å: Chain B: D.203, W.204, V.233, E.239, Y.243 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.204, B:G.206, B:E.239, B:E.239 GOL.18: 8 residues within 4Å: Chain B: H.121, N.162, E.163, H.229, Y.231, A.258, W.288 Ligands: BMA-BMA-BMA.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.162, B:E.163, B:H.229, B:Y.231

7 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.5: 14 residues within 4Å: Chain A: H.121, N.162, E.163, H.229, Y.231, A.258, W.288, N.293, L.298 Ligands: BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA.6, BMA.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.121, A:N.162, A:E.163, A:Y.231 Water bridges: A:E.163, A:H.229 BMA.6: 12 residues within 4Å: Chain A: W.65, W.94, H.121, W.288, G.292, N.293, T.294 Ligands: BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA.5, BMA.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.288, A:G.292, A:T.294, A:T.294 Water bridges: A:R.93, A:D.295 BMA.7: 10 residues within 4Å: Chain A: W.65, Y.66, W.94, G.292, T.294 Ligands: BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA.6, BMA.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.66, A:Y.66, A:W.94 Water bridges: A:T.294 BMA.8: 4 residues within 4Å: Chain A: W.65 Ligands: BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.65 BMA.9: 7 residues within 4Å: Chain A: N.167, W.204, V.233, W.266 Ligands: BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.167 Water bridges: A:V.233 BMA.10: 11 residues within 4Å: Chain A: N.167, N.199, W.200, Q.202, W.204, W.266 Ligands: BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA.9, BMA.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.167, A:Q.202, A:W.204 BMA.11: 9 residues within 4Å: Chain A: E.163, W.200, Q.202, Y.231 Ligands: BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA-BMA-BMA-BMA-BMA-BMA-BMA.1, BMA.5, BMA.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.202

5 x CA: CALCIUM ION(Non-covalent)

CA.12: 3 residues within 4Å: Chain A: V.233, D.235, E.239 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.233, A:D.235, A:E.239, A:E.239, H2O.12 CA.13: 4 residues within 4Å: Chain A: G.261, D.268, P.269, E.271 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.261, A:D.268, A:P.269, A:E.271, H2O.11 CA.19: 4 residues within 4Å: Chain B: G.261, D.268, P.269, E.271 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.261, B:D.268, B:P.269, B:E.271, H2O.26 CA.20: 3 residues within 4Å: Chain B: V.233, D.235, E.239 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:V.233, B:D.235, H2O.21, H2O.25, H2O.27 CA.21: 1 residues within 4Å: Chain B: K.183 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumagai, Y. et al., The loop structure of Actinomycete glycoside hydrolase family 5 mannanases governs substrate recognition. Febs J. (2015)

Release Date

2015-09-23

Peptides

Endoglucanase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endoglucanase

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