3DKD
Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with GDP
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B (A, B) | Nucleoside diphosphate kinase | polymer | 146 | 16527.7 | 2 | UniProt (Q5UQL3) Pfam (PF00334) | Acanthamoeba polyphaga mimivirus (APMV) | NDP kinase, NDK |
| 2 | C, E (A, B) | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) PubChem (888) | |||
| 3 | D, F (A, B) | GUANOSINE-5'-DIPHOSPHATE | non-polymer | 443.2 | 2 | Chemie (GDP) PubChem (136073927) PubChem (135398619) PubChem (135402030) PubChem (135431654) PubChem (135566337) PubChem (135760556) PubChem (136026707) PubChem (136053418) PubChem (136663964) PubChem (136664748) PubChem (136759848) PubChem (136759849) PubChem (136759850) PubChem (136836636) PubChem (136847074) PubChem (172898537) | |||
| 4 | G, H (A, B) | water | water | 18.0 | 248 | Chemie (HOH) |
Sequence modifications
A, B: 2 - 141 (UniProt: Q5UQL3)
| PDB | External Database | Details |
|---|---|---|
| Tyr -4 | - | expression tag |
| Lys -3 | - | expression tag |
| Lys -2 | - | expression tag |
| Ala -1 | - | expression tag |
| Gly 0 | - | expression tag |
| Leu 1 | - | expression tag |
| Leu 62 | Asn 62 | engineered mutation |
| Thr 92 | - | SEE REMARK 999 |
| Asn 93 | - | SEE REMARK 999 |
| Pro 94 | - | SEE REMARK 999 |
| Leu 95 | - | SEE REMARK 999 |
| Ala 96 | Ile 92 | SEE REMARK 999 |
| Ser 97 | Leu 93 | SEE REMARK 999 |
| Ala 98 | Thr 94 | SEE REMARK 999 |
| Gly 111 | Arg 107 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total formula weight | 33055.4 | |
| Non-Polymers* | Number of molecules | 4 |
| Total formula weight | 935.0 | |
| All* | Total formula weight | 33990.4 |
