Finding GlcSFMs for Glucides in the PDB entry '1OGD' ... |
PDB Entry | Title | Determination Method | Resolution | R-Factor |
1OGD | THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH D-RIBOSE | X-RAY | 1.95 | 0.198
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| 1OGD has 4 GlcSFMs: |
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| Motif No. / Chain | Motif | Bound Ligand /(Nbr. in PDB) | Show Details |
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| 1 / A |
> Structure: LLLLHLLL
+2w
> Sequence: DGLPHPYN
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RIP /(1134) |
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Protein Chain | Prot SSE | Res Nbr | Res Name | RsAt.Name | LgAt.Name |
Lg Chain | Lg Nbr | Bnd Len | Bnd Type |
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A | No SSE | 28 | ASP | CG | C2 | A | 1134 | 3.99 | van der Waals | A | No SSE | 28 | ASP | CG | O2 | A | 1134 | 3.38 | van der Waals | A | No SSE | 28 | ASP | CG | O3 | A | 1134 | 3.48 | van der Waals | A | No SSE | 28 | ASP | OD1 | C2 | A | 1134 | 3.67 | van der Waals | A | No SSE | 28 | ASP | OD1 | C3 | A | 1134 | 3.6 | van der Waals | A | No SSE | 28 | ASP | OD1 | O2 | A | 1134 | 3.37 | H.Bond | A | No SSE | 28 | ASP | OD1 | O3 | A | 1134 | 2.48 | H.Bond | A | No SSE | 28 | ASP | OD2 | C2 | A | 1134 | 3.46 | van der Waals | A | No SSE | 28 | ASP | OD2 | O2 | A | 1134 | 2.7 | H.Bond | A | No SSE | 28 | ASP | OD2 | O3 | A | 1134 | 3.76 | H.Bond | A | No SSE | 30 | GLY | N | O2 | A | 1134 | 3.76 | H.Bond | A | No SSE | 30 | GLY | CA | O2 | A | 1134 | 3.3 | van der Waals | A | No SSE | 30 | GLY | C | C1 | A | 1134 | 3.86 | van der Waals | A | No SSE | 30 | GLY | C | C2 | A | 1134 | 3.84 | van der Waals | A | No SSE | 30 | GLY | C | O2 | A | 1134 | 3.27 | van der Waals | A | No SSE | 30 | GLY | O | C1 | A | 1134 | 3.78 | van der Waals | A | No SSE | 30 | GLY | O | O2 | A | 1134 | 3.87 | H.Bond | A | No SSE | 31 | LEU | N | C1 | A | 1134 | 3.98 | H.Bond | A | No SSE | 31 | LEU | N | C2 | A | 1134 | 3.66 | H.Bond | A | No SSE | 31 | LEU | N | O2 | A | 1134 | 3.35 | H.Bond | A | No SSE | 31 | LEU | CA | C2 | A | 1134 | 3.92 | van der Waals | A | No SSE | 31 | LEU | CD1 | O1 | A | 1134 | 3.93 | van der Waals | A | No SSE | 32 | PRO | CD | O1 | A | 1134 | 3.88 | van der Waals | A | 97-105 H: 1 | 98 | HIS | CD2 | O1 | A | 1134 | 3.98 | van der Waals | A | 97-105 H: 1 | 98 | HIS | CE1 | C3 | A | 1134 | 3.94 | van der Waals | A | 97-105 H: 1 | 98 | HIS | CE1 | O1 | A | 1134 | 3.43 | van der Waals | A | 97-105 H: 1 | 98 | HIS | NE2 | O1 | A | 1134 | 2.84 | H.Bond | A | No SSE | 119 | PRO | C | O3 | A | 1134 | 3.88 | van der Waals | A | No SSE | 120 | TYR | N | C3 | A | 1134 | 3.82 | H.Bond | A | No SSE | 120 | TYR | N | C4 | A | 1134 | 3.98 | H.Bond | A | No SSE | 120 | TYR | N | O3 | A | 1134 | 2.73 | H.Bond | A | No SSE | 120 | TYR | CA | O3 | A | 1134 | 3.04 | van der Waals | A | No SSE | 120 | TYR | C | O3 | A | 1134 | 3.98 | van der Waals | A | No SSE | 122 | ASN | OD1 | C3 | A | 1134 | 3.91 | van der Waals | A | No SSE | 122 | ASN | OD1 | O3 | A | 1134 | 3.19 | H.Bond | A | Water | 2032 | HOH | O | C1 | A | 1134 | 3.76 | van der Waals | A | Water | 2032 | HOH | O | O1 | A | 1134 | 2.86 | H.Bond | A | Water | 2032 | HOH | O | O5 | A | 1134 | 3.74 | H.Bond | A | Water | 2033 | HOH | O | C4 | A | 1134 | 3.69 | van der Waals | A | Water | 2033 | HOH | O | C5 | A | 1134 | 3.95 | van der Waals | A | Water | 2033 | HOH | O | O4 | A | 1134 | 2.96 | H.Bond | |
| 2 / B |
> Structure: LLLLHLLLL
+1w
> Sequence: DGLPHPYAN
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RIP /(1132) |
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Protein Chain | Prot SSE | Res Nbr | Res Name | RsAt.Name | LgAt.Name |
Lg Chain | Lg Nbr | Bnd Len | Bnd Type |
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B | No SSE | 28 | ASP | CG | O2 | B | 1132 | 3.39 | van der Waals | B | No SSE | 28 | ASP | CG | O3 | B | 1132 | 3.46 | van der Waals | B | No SSE | 28 | ASP | OD1 | C2 | B | 1132 | 3.76 | van der Waals | B | No SSE | 28 | ASP | OD1 | C3 | B | 1132 | 3.62 | van der Waals | B | No SSE | 28 | ASP | OD1 | O2 | B | 1132 | 3.37 | H.Bond | B | No SSE | 28 | ASP | OD1 | O3 | B | 1132 | 2.47 | H.Bond | B | No SSE | 28 | ASP | OD2 | C2 | B | 1132 | 3.52 | van der Waals | B | No SSE | 28 | ASP | OD2 | O2 | B | 1132 | 2.71 | H.Bond | B | No SSE | 28 | ASP | OD2 | O3 | B | 1132 | 3.72 | H.Bond | B | No SSE | 30 | GLY | N | O2 | B | 1132 | 3.78 | H.Bond | B | No SSE | 30 | GLY | CA | O2 | B | 1132 | 3.31 | van der Waals | B | No SSE | 30 | GLY | C | C1 | B | 1132 | 3.87 | van der Waals | B | No SSE | 30 | GLY | C | C2 | B | 1132 | 3.78 | van der Waals | B | No SSE | 30 | GLY | C | O2 | B | 1132 | 3.22 | van der Waals | B | No SSE | 30 | GLY | O | C1 | B | 1132 | 3.7 | van der Waals | B | No SSE | 30 | GLY | O | O2 | B | 1132 | 3.77 | H.Bond | B | No SSE | 31 | LEU | N | C2 | B | 1132 | 3.62 | H.Bond | B | No SSE | 31 | LEU | N | O2 | B | 1132 | 3.3 | H.Bond | B | No SSE | 31 | LEU | CA | C2 | B | 1132 | 3.84 | van der Waals | B | No SSE | 32 | PRO | CD | O1 | B | 1132 | 3.88 | van der Waals | B | 97-105 H: 1 | 98 | HIS | CD2 | O1 | B | 1132 | 3.98 | van der Waals | B | 97-105 H: 1 | 98 | HIS | CE1 | C3 | B | 1132 | 3.93 | van der Waals | B | 97-105 H: 1 | 98 | HIS | CE1 | O1 | B | 1132 | 3.69 | van der Waals | B | 97-105 H: 1 | 98 | HIS | NE2 | C3 | B | 1132 | 3.91 | H.Bond | B | 97-105 H: 1 | 98 | HIS | NE2 | O1 | B | 1132 | 2.93 | H.Bond | B | No SSE | 119 | PRO | CA | O4 | B | 1132 | 3.81 | van der Waals | B | No SSE | 119 | PRO | C | O3 | B | 1132 | 3.88 | van der Waals | B | No SSE | 120 | TYR | N | C3 | B | 1132 | 3.79 | H.Bond | B | No SSE | 120 | TYR | N | C4 | B | 1132 | 3.8 | H.Bond | B | No SSE | 120 | TYR | N | O3 | B | 1132 | 2.78 | H.Bond | B | No SSE | 120 | TYR | N | O4 | B | 1132 | 3.91 | H.Bond | B | No SSE | 120 | TYR | CA | O3 | B | 1132 | 3.11 | van der Waals | B | No SSE | 120 | TYR | C | O3 | B | 1132 | 3.97 | van der Waals | B | No SSE | 121 | ALA | N | O3 | B | 1132 | 3.93 | H.Bond | B | No SSE | 122 | ASN | OD1 | C3 | B | 1132 | 3.91 | van der Waals | B | No SSE | 122 | ASN | OD1 | O3 | B | 1132 | 3.07 | H.Bond | B | Water | 2034 | HOH | O | C1 | B | 1132 | 3.77 | van der Waals | B | Water | 2034 | HOH | O | O1 | B | 1132 | 2.75 | H.Bond | B | Water | 2034 | HOH | O | O5 | B | 1132 | 3.92 | H.Bond | |
| 3 / C |
> Structure: LLLLHLLL
+2w
> Sequence: DGLPHPYN
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RIP /(1132) |
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Protein Chain | Prot SSE | Res Nbr | Res Name | RsAt.Name | LgAt.Name |
Lg Chain | Lg Nbr | Bnd Len | Bnd Type |
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C | No SSE | 28 | ASP | CG | O2 | C | 1132 | 3.39 | van der Waals | C | No SSE | 28 | ASP | CG | O3 | C | 1132 | 3.45 | van der Waals | C | No SSE | 28 | ASP | OD1 | C2 | C | 1132 | 3.76 | van der Waals | C | No SSE | 28 | ASP | OD1 | C3 | C | 1132 | 3.6 | van der Waals | C | No SSE | 28 | ASP | OD1 | O2 | C | 1132 | 3.33 | H.Bond | C | No SSE | 28 | ASP | OD1 | O3 | C | 1132 | 2.46 | H.Bond | C | No SSE | 28 | ASP | OD2 | C2 | C | 1132 | 3.52 | van der Waals | C | No SSE | 28 | ASP | OD2 | O2 | C | 1132 | 2.74 | H.Bond | C | No SSE | 28 | ASP | OD2 | O3 | C | 1132 | 3.7 | H.Bond | C | No SSE | 30 | GLY | N | O2 | C | 1132 | 3.73 | H.Bond | C | No SSE | 30 | GLY | CA | O2 | C | 1132 | 3.31 | van der Waals | C | No SSE | 30 | GLY | C | C1 | C | 1132 | 3.84 | van der Waals | C | No SSE | 30 | GLY | C | C2 | C | 1132 | 3.75 | van der Waals | C | No SSE | 30 | GLY | C | O2 | C | 1132 | 3.26 | van der Waals | C | No SSE | 30 | GLY | O | C1 | C | 1132 | 3.71 | van der Waals | C | No SSE | 30 | GLY | O | O2 | C | 1132 | 3.85 | H.Bond | C | No SSE | 31 | LEU | N | C2 | C | 1132 | 3.58 | H.Bond | C | No SSE | 31 | LEU | N | O2 | C | 1132 | 3.32 | H.Bond | C | No SSE | 31 | LEU | CA | C2 | C | 1132 | 3.83 | van der Waals | C | No SSE | 32 | PRO | CD | O1 | C | 1132 | 3.88 | van der Waals | C | 97-105 H: 1 | 98 | HIS | CE1 | C3 | C | 1132 | 3.91 | van der Waals | C | 97-105 H: 1 | 98 | HIS | CE1 | O1 | C | 1132 | 3.74 | van der Waals | C | 97-105 H: 1 | 98 | HIS | NE2 | O1 | C | 1132 | 3.19 | H.Bond | C | No SSE | 119 | PRO | CA | O4 | C | 1132 | 3.9 | van der Waals | C | No SSE | 120 | TYR | N | C3 | C | 1132 | 3.88 | H.Bond | C | No SSE | 120 | TYR | N | C4 | C | 1132 | 3.8 | H.Bond | C | No SSE | 120 | TYR | N | O3 | C | 1132 | 2.89 | H.Bond | C | No SSE | 120 | TYR | N | O4 | C | 1132 | 3.79 | H.Bond | C | No SSE | 120 | TYR | CA | O3 | C | 1132 | 3.09 | van der Waals | C | No SSE | 120 | TYR | C | O3 | C | 1132 | 3.98 | van der Waals | C | No SSE | 122 | ASN | OD1 | C3 | C | 1132 | 3.84 | van der Waals | C | No SSE | 122 | ASN | OD1 | O3 | C | 1132 | 2.97 | H.Bond | C | Water | 2046 | HOH | O | C1 | C | 1132 | 3.85 | van der Waals | C | Water | 2046 | HOH | O | O1 | C | 1132 | 2.77 | H.Bond | C | Water | 2047 | HOH | O | C4 | C | 1132 | 3.81 | van der Waals | C | Water | 2047 | HOH | O | C5 | C | 1132 | 3.93 | van der Waals | C | Water | 2047 | HOH | O | O4 | C | 1132 | 2.91 | H.Bond | |
| 4 / D |
> Structure: LLLHLLLL
+1w
> Sequence: DGLHPYAN
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RIP /(1132) |
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Protein Chain | Prot SSE | Res Nbr | Res Name | RsAt.Name | LgAt.Name |
Lg Chain | Lg Nbr | Bnd Len | Bnd Type |
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D | No SSE | 28 | ASP | CG | O2 | D | 1132 | 3.45 | van der Waals | D | No SSE | 28 | ASP | CG | O3 | D | 1132 | 3.41 | van der Waals | D | No SSE | 28 | ASP | OD1 | C2 | D | 1132 | 3.73 | van der Waals | D | No SSE | 28 | ASP | OD1 | C3 | D | 1132 | 3.56 | van der Waals | D | No SSE | 28 | ASP | OD1 | O2 | D | 1132 | 3.42 | H.Bond | D | No SSE | 28 | ASP | OD1 | O3 | D | 1132 | 2.4 | H.Bond | D | No SSE | 28 | ASP | OD2 | C2 | D | 1132 | 3.53 | van der Waals | D | No SSE | 28 | ASP | OD2 | O2 | D | 1132 | 2.77 | H.Bond | D | No SSE | 28 | ASP | OD2 | O3 | D | 1132 | 3.68 | H.Bond | D | No SSE | 30 | GLY | N | O2 | D | 1132 | 3.87 | H.Bond | D | No SSE | 30 | GLY | CA | O2 | D | 1132 | 3.43 | van der Waals | D | No SSE | 30 | GLY | C | C2 | D | 1132 | 3.86 | van der Waals | D | No SSE | 30 | GLY | C | O2 | D | 1132 | 3.3 | van der Waals | D | No SSE | 30 | GLY | O | C1 | D | 1132 | 3.8 | van der Waals | D | No SSE | 30 | GLY | O | O2 | D | 1132 | 3.79 | H.Bond | D | No SSE | 31 | LEU | N | C2 | D | 1132 | 3.74 | H.Bond | D | No SSE | 31 | LEU | N | O2 | D | 1132 | 3.44 | H.Bond | D | No SSE | 31 | LEU | CA | C2 | D | 1132 | 3.92 | van der Waals | D | 97-105 H: 1 | 98 | HIS | CD2 | O1 | D | 1132 | 3.97 | van der Waals | D | 97-105 H: 1 | 98 | HIS | CE1 | C3 | D | 1132 | 3.93 | van der Waals | D | 97-105 H: 1 | 98 | HIS | CE1 | O1 | D | 1132 | 3.52 | van der Waals | D | 97-105 H: 1 | 98 | HIS | NE2 | O1 | D | 1132 | 2.86 | H.Bond | D | No SSE | 119 | PRO | CA | O4 | D | 1132 | 3.9 | van der Waals | D | No SSE | 119 | PRO | C | O3 | D | 1132 | 3.97 | van der Waals | D | No SSE | 120 | TYR | N | C3 | D | 1132 | 3.79 | H.Bond | D | No SSE | 120 | TYR | N | C4 | D | 1132 | 3.73 | H.Bond | D | No SSE | 120 | TYR | N | O3 | D | 1132 | 2.81 | H.Bond | D | No SSE | 120 | TYR | N | O4 | D | 1132 | 3.8 | H.Bond | D | No SSE | 120 | TYR | CA | O3 | D | 1132 | 3.03 | van der Waals | D | No SSE | 120 | TYR | C | O3 | D | 1132 | 3.9 | van der Waals | D | No SSE | 121 | ALA | N | O3 | D | 1132 | 3.92 | H.Bond | D | No SSE | 122 | ASN | OD1 | C3 | D | 1132 | 3.89 | van der Waals | D | No SSE | 122 | ASN | OD1 | O3 | D | 1132 | 3.02 | H.Bond | D | Water | 2045 | HOH | O | C1 | D | 1132 | 3.79 | van der Waals | D | Water | 2045 | HOH | O | O1 | D | 1132 | 2.78 | H.Bond | |