SMTL ID : 1ogf.1

The Structure of Bacillus subtilis RbsD complexed with glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-10-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 Chain E: H.20, F.131 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:D.28, A:Y.120, A:N.122, E:H.20 GOL.3: 9 residues within 4Å: Chain A: H.20, V.129 Chain B: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.28, B:Y.120, B:N.122, A:H.20 GOL.4: 9 residues within 4Å: Chain B: H.20, V.129 Chain C: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.28, C:Y.120, C:N.122, B:H.20 GOL.5: 10 residues within 4Å: Chain C: H.20, V.129, F.131 Chain D: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.28, D:Y.120, D:N.122, C:H.20 GOL.6: 9 residues within 4Å: Chain D: H.20, F.131 Chain E: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:H.20, E:D.28, E:Y.120, E:N.122 Water bridges: E:Y.120, E:Y.120 GOL.8: 9 residues within 4Å: Chain F: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 Chain J: H.20, F.131 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:D.28, F:Y.120, F:N.122, J:H.20 GOL.10: 9 residues within 4Å: Chain F: H.20, V.129 Chain G: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:H.20, G:D.28, G:Y.120, G:N.122 GOL.11: 9 residues within 4Å: Chain G: H.20, V.129 Chain H: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:D.28, H:Y.120, H:N.122, G:H.20 Water bridges: H:Y.120 GOL.12: 10 residues within 4Å: Chain H: H.20, V.129, F.131 Chain I: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:H.20, I:D.28, I:Y.120, I:N.122 GOL.13: 9 residues within 4Å: Chain I: H.20, F.131 Chain J: D.28, G.30, L.31, H.98, P.119, Y.120, N.122 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:D.28, J:Y.120, J:N.122, I:H.20

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

CL.2: 2 residues within 4Å: Chain A: K.2 Chain H: K.2 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain D: K.2 Chain J: K.2 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain C: K.2 Chain F: K.2 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain E: K.2 Chain I: K.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, M.-S. et al., Crystal Structures of Rbsd Leading to the Identification of Cytoplasmic Sugar-Binding Proteins with a Novel Folding Architecture. J.Biol.Chem. (2003)

Release Date

2003-09-01

Peptides

HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD

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