SMTL ID : 1ogd.1

The Structure of Bacillus subtilis RbsD complexed with D-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-10-mer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: K.2, H.4 Chain H: K.2, H.4 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain D: K.2, H.4 Chain J: K.2, H.4 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain C: K.2, H.4 Chain F: K.2, H.4 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain E: K.2, H.4 Chain I: K.2, H.4 Ligand excluded by PLIP

10 x RIP: beta-D-ribopyranose(Non-covalent)

RIP.2: 10 residues within 4Å: Chain A: D.28, G.30, L.31, P.32, H.98, P.119, Y.120, N.122 Chain E: H.20, F.131 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:G.30, A:G.30, A:Y.120, A:A.121, A:N.122 Salt bridges: A:H.98, E:H.20 Water bridges: E:H.20 RIP.3: 11 residues within 4Å: Chain A: H.20, F.131 Chain B: D.28, G.30, L.31, P.32, H.98, P.119, Y.120, A.121, N.122 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.30, B:G.30, B:Y.120, B:A.121, B:N.122 Salt bridges: B:H.98, A:H.20 RIP.4: 10 residues within 4Å: Chain B: H.20, F.131 Chain C: D.28, G.30, L.31, P.32, H.98, P.119, Y.120, N.122 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.30, C:G.30, C:Y.120, C:A.121, C:N.122 Salt bridges: C:H.98, B:H.20 RIP.5: 10 residues within 4Å: Chain C: H.20, F.131 Chain D: D.28, G.30, L.31, H.98, P.119, Y.120, A.121, N.122 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.30, D:G.30, D:Y.120, D:A.121, D:N.122 Salt bridges: D:H.98, C:H.20 Water bridges: C:H.20 RIP.7: 10 residues within 4Å: Chain D: H.20, F.131 Chain E: D.28, G.30, L.31, P.32, H.98, P.119, Y.120, N.122 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.30, E:G.30, E:Y.120, E:A.121, E:N.122 Salt bridges: E:H.98, D:H.20 Water bridges: D:H.20 RIP.9: 10 residues within 4Å: Chain F: D.28, G.30, L.31, P.32, H.98, P.119, Y.120, N.122 Chain J: H.20, F.131 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:G.30, F:G.30, F:Y.120, F:A.121, F:N.122 Salt bridges: F:H.98, J:H.20 RIP.10: 11 residues within 4Å: Chain F: H.20, F.131 Chain G: D.28, G.30, L.31, P.32, H.98, P.119, Y.120, A.121, N.122 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:G.30, G:G.30, G:Y.120, G:A.121, G:N.122 Salt bridges: G:H.98, F:H.20 Water bridges: F:H.20 RIP.11: 10 residues within 4Å: Chain G: H.20, F.131 Chain H: D.28, G.30, L.31, P.32, H.98, P.119, Y.120, N.122 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:G.30, H:G.30, H:Y.120, H:A.121, H:N.122 Salt bridges: H:H.98, G:H.20 Water bridges: G:H.20 RIP.12: 10 residues within 4Å: Chain H: H.20, F.131 Chain I: D.28, G.30, L.31, H.98, P.119, Y.120, A.121, N.122 7 PLIP interactions: 6 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:G.30, I:G.30, I:Y.120, I:A.121, I:N.122 Salt bridges: I:H.98, H:H.20 RIP.14: 10 residues within 4Å: Chain I: H.20, F.131 Chain J: D.28, G.30, L.31, P.32, H.98, P.119, Y.120, N.122 7 PLIP interactions: 6 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:G.30, J:G.30, J:Y.120, J:A.121, J:N.122 Salt bridges: J:H.98, I:H.20

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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