SMTL ID : 3etn.1

Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x CMK: CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID(Non-covalent)

CMK.1: 14 residues within 4Å: Chain A: M.67, G.68, K.69, A.70, S.114, N.115, S.116, K.118, T.119, P.172 Chain B: H.206, G.208, Y.209 Chain C: H.98 19 PLIP interactions: 3 interactions with chain B, 15 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:Y.209, A:A.70, A:N.115, A:N.115, A:S.116, A:S.116, A:K.118, A:T.119 Water bridges: B:H.206, A:K.69, A:K.69, A:T.119, A:R.120, A:E.164, A:S.175, A:S.175 Salt bridges: B:H.206, C:H.98 Hydrophobic interactions: A:K.118 CMK.5: 14 residues within 4Å: Chain A: H.206, G.208, Y.209 Chain B: M.67, G.68, K.69, A.70, S.114, N.115, S.116, K.118, T.119, P.172 Chain D: H.98 18 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:K.118 Hydrogen bonds: B:A.70, B:N.115, B:N.115, B:S.116, B:S.116, B:K.118, A:Y.209 Water bridges: B:K.69, B:T.119, B:R.120, B:R.120, B:S.175, B:S.175, A:H.206, A:Y.209 Salt bridges: A:H.206, D:H.98 CMK.9: 14 residues within 4Å: Chain A: H.98 Chain C: M.67, G.68, K.69, A.70, S.114, N.115, S.116, K.118, T.119, P.172 Chain D: H.206, G.208, Y.209 18 PLIP interactions: 3 interactions with chain D, 14 interactions with chain C, 1 interactions with chain A Water bridges: D:H.206, D:Y.209, C:T.119, C:R.120, C:S.175, C:S.175 Salt bridges: D:H.206, A:H.98 Hydrophobic interactions: C:K.118 Hydrogen bonds: C:K.69, C:A.70, C:N.115, C:N.115, C:S.116, C:S.116, C:K.118, C:K.118, C:T.119 CMK.11: 14 residues within 4Å: Chain B: H.98 Chain C: H.206, G.208, Y.209 Chain D: M.67, G.68, K.69, A.70, S.114, N.115, S.116, K.118, T.119, P.172 18 PLIP interactions: 14 interactions with chain D, 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:K.118 Hydrogen bonds: D:K.69, D:A.70, D:N.115, D:N.115, D:S.116, D:S.116, D:K.118 Water bridges: D:K.118, D:K.118, D:T.119, D:R.120, D:S.175, D:S.175, C:H.206, C:Y.209 Salt bridges: C:H.206, B:H.98

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

EDO.2: 3 residues within 4Å: Chain A: R.120 Chain B: H.206 Chain C: Q.97 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Water bridges: C:H.98, A:R.120, A:E.121, A:E.121 EDO.3: 3 residues within 4Å: Chain A: Q.97 Chain C: R.120 Chain D: H.206 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.121 Water bridges: C:R.120 EDO.4: 4 residues within 4Å: Chain A: Q.25, L.28, Q.29 Chain B: L.36 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.25 Hydrogen bonds: B:L.36 EDO.6: 4 residues within 4Å: Chain B: A.150, S.151, S.153, C.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.153 EDO.7: 3 residues within 4Å: Chain B: H.130, N.131, P.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.127, B:H.130, B:N.131 EDO.8: 7 residues within 4Å: Chain B: P.39, V.40, T.41, Y.44, C.156, L.157, S.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.41, B:S.158 Water bridges: B:T.41 EDO.10: 4 residues within 4Å: Chain C: A.150, S.151, S.153, D.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.151 Water bridges: C:C.156 EDO.12: 8 residues within 4Å: Chain D: P.39, V.40, T.41, A.43, Y.44, C.156, L.157, S.158 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.41, D:T.41, D:S.158 EDO.13: 4 residues within 4Å: Chain D: E.49, E.53, R.57, R.193 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.53, D:R.57, D:R.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiu, H.J. et al., Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications. Acta Crystallogr.,Sect.D (2014)

Release Date

2008-10-21

Peptides

putative phosphosugar isomerase involved in capsule formation: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

putative phosphosugar isomerase involved in capsule formation