SMTL ID : 4u6b.1

Zg3597, a family 117 glycoside hydrolase, produced by the marine bacterium Zobellia galactanivorans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 6 residues within 4Å: Chain A: E.78, D.397, S.399, V.402, D.403, K.408 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.78, A:D.397, A:D.397, A:V.402, H2O.5 CA.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.7: 5 residues within 4Å: Chain B: E.78, D.397, S.399, V.402, D.403 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.397, B:S.399, B:V.402, H2O.10, H2O.10 CA.8: 1 residues within 4Å: Chain B: P.105 No protein-ligand interaction detected (PLIP) CA.13: 6 residues within 4Å: Chain C: E.78, D.397, S.399, V.402, D.403, K.408 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.78, C:D.397, C:D.397, C:S.399, C:V.402 CA.14: 1 residues within 4Å: Chain C: P.105 No protein-ligand interaction detected (PLIP) CA.18: 4 residues within 4Å: Chain D: E.78, D.397, S.399, V.402 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.397, D:S.399, H2O.26, H2O.27, H2O.27 CA.19: 1 residues within 4Å: Chain D: P.105 No protein-ligand interaction detected (PLIP)

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

PEG.3: 8 residues within 4Å: Chain A: R.103, D.104, W.146, T.184, Q.199, D.249, K.264, E.307 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.103, A:T.184, A:K.264, A:K.264 Water bridges: A:W.146, A:H.248 PEG.4: 7 residues within 4Å: Chain A: A.137, D.139, K.174, W.179, R.180, P.204 Chain C: K.239 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.137, A:D.139, A:R.180, C:K.239

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

EDO.5: 9 residues within 4Å: Chain A: H.248, D.249, Q.251, Y.262, Y.263, K.264, H.281, T.308, Y.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.262 Water bridges: A:D.249, A:Q.251 EDO.10: 7 residues within 4Å: Chain B: D.249, Q.251, Y.262, Y.263, H.281, T.308, Y.310 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.308, B:T.308 Water bridges: B:P.250, B:Q.251, B:T.308, B:T.308, B:T.309 EDO.11: 3 residues within 4Å: Chain B: R.103, D.249, K.264 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.264 EDO.12: 2 residues within 4Å: Chain B: G.113, E.157 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.157 Water bridges: B:E.157 EDO.15: 2 residues within 4Å: Chain C: D.123, R.171 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.171 Water bridges: C:D.123, C:D.123, C:D.123 EDO.16: 4 residues within 4Å: Chain C: K.256, G.257, K.258, D.287 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.258, C:D.287 EDO.17: 6 residues within 4Å: Chain C: D.249, Q.251, Y.262, Y.263, H.281, T.308 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.308 Water bridges: C:Q.251, C:T.308, C:T.308 EDO.20: 3 residues within 4Å: Chain C: E.417, F.420 Chain D: R.87 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.87, D:R.87 EDO.21: 3 residues within 4Å: Chain D: Y.153, E.165, V.167 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.153, D:V.167 Water bridges: D:E.165 EDO.22: 1 residues within 4Å: Chain D: D.123 4 PLIP interactions: 4 interactions with chain D Water bridges: D:D.123, D:D.123, D:T.124, D:T.124

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

NA.6: 5 residues within 4Å: Chain A: A.286, D.287, D.288, G.291, P.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.287, A:D.288, A:D.288

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.9: 6 residues within 4Å: Chain A: H.414, Y.419 Chain B: T.351, F.377, T.378, N.379 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.377 Hydrogen bonds: B:T.378, B:N.379 Water bridges: B:T.378, B:T.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ficko-Blean, E. et al., Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-02-11

Peptides

Conserved hypothetical lipoprotein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Conserved hypothetical lipoprotein