3RUN
New strategy to analyze structures of glycopeptide antibiotic-target complexes
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | LYSOZYME | polymer | 168 | 19018.8 | 1 | UniProt (P00720) Pfam (PF00959) | ENTEROBACTERIA PHAGE T4 | Endolysin, Lysis protein, Muramidase |
| 2 | B (B) | VANCOMYCIN | polymer | 7 | 1150.0 | 1 | NOR (NOR00681) BIRD (PRD_000204) | Streptomyces orientalis | |
| 3 | C (C) | vancosamine-(1-2)-beta-D-glucopyranose | branched | 323.3 | 1 | In PDB BIRD (PRD_000204) GlyTouCan (G14263HU) | |||
| 4 | D (A) | (4S)-2-METHYL-2,4-PENTANEDIOL | non-polymer | 118.2 | 1 | Chemie (MPD) | |||
| 5 | E, K (A, B) | (4R)-2-METHYLPENTANE-2,4-DIOL | non-polymer | 118.2 | 2 | Chemie (MRD) | |||
| 6 | F (A) | PHOSPHATE ION | non-polymer | 95.0 | 1 | Chemie (PO4) | |||
| 7 | G (A) | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL | non-polymer | 122.1 | 1 | Chemie (TRS) | |||
| 8 | H (A) | CHLORIDE ION | non-polymer | 35.5 | 1 | Chemie (CL) | |||
| 9 | I, J (A) | ISOPROPYL ALCOHOL | non-polymer | 60.1 | 2 | Chemie (IPA) | |||
| 10 | L, M (A, B) | water | water | 18.0 | 316 | Chemie (HOH) |
Sequence modifications
A: 1 - 164 (UniProt: P00720)
| PDB | External Database | Details |
|---|---|---|
| Thr 54 | Cys 54 | engineered mutation |
| Ala 97 | Cys 97 | engineered mutation |
| Ala 164 | Leu 164 | engineered mutation |
| Ccs 165 | - | SEE REMARK 999 |
| Lys 166 | - | SEE REMARK 999 |
| Dal 167 | - | SEE REMARK 999 |
| Dal 168 | - | SEE REMARK 999 |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total formula weight | 20168.8 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 323.3 | |
| Non-Polymers* | Number of molecules | 8 |
| Total formula weight | 727.3 | |
| All* | Total formula weight | 21219.4 |
