PDBsum entry 2zdq

Go to PDB code: 
Top Page protein ligands Protein-protein interface(s) links
Ligase PDB id
Protein chains
319 a.a.
ATP ×2
Waters ×194

References listed in PDB file
Key reference
Title Crystal structure of d-Alanine:d-Alanine ligase with atp and d-Alanine:d-Alanine from thermus thermophius hb8
Authors Y.Kitamura, S.Yokoyama, S.Kuramitsu.
Ref. To be Published ...
Added reference #1*
Title Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions.
Authors Y.Kitamura, A.Ebihara, Y.Agari, A.Shinkai, K.Hirotsu, S.Kuramitsu.
Ref. Acta Crystallogr D Biol Crystallogr, 2009, 65, 1098-1106. [DOI no: 10.1107/S0907444909029710]
PubMed id 19770507
Full text Abstract
Figure 3.
Figure 3 Overall structure of TtDdl. ATP and D-Ala-D-Ala are shown as ball-and-stick models. (a) Ribbon structural drawing of unliganded TtDdl in the open form. ATP and D-Ala-D-Ala are modelled into the active site by superposing TtDdl-ATP-D-Ala-D-Ala onto unliganded TtDdl. The N-terminal, central and C-terminal domains and loops (loops I, II and III) are shown as yellow, cyan, green and red ribbons, respectively. -Strands are denoted by 1- 15 and -helices by 1- 10. The N- and C-termini are labelled. (b) Superposed backbone structures. The molecular structures of unliganded TtDdl in the open form (grey), TtDdl-ADP in the semi-open form (orange), TtDdl-ADP-D-Ala in the semi-closed form (cyan) and TtDdl-ATP-D-Ala-D-Ala in the closed form (magenta) forms were superimposed by fitting the C^ atoms of the N- and C-terminal domains. The loops are represented by bold lines.
Figure 4.
Figure 4 Stereo diagram of the active site in TtDdl. Each figure is viewed from the solvent side (the entrance to the active site). The active-site residues are represented by stick models. Water molecules are drawn as cyan circles. The N-terminal, central and C-terminal domains are drawn in yellow, blue and grey, respectively. Dotted lines represent coordination or hydrogen bonds. (a) Active site of TtDdl-ADP-D-Ala. ADP and D-Ala are shown as stick models. Mg ions are represented by red circles. The 2F[o] - F[c] electron-density map contoured at 1.0 was calculated using data to 1.9 Å resolution. (b) Active site of TtDdl-ATP-D-Ala-D-Ala. ATP and D-Ala-D-Ala are shown as stick models. Loop III in TtDdl-ADP-D-Ala (red) is superimposed. (c) Surface representation of the D-Ala channel in TtDdl-ADP-D-Ala. Loops II and III are shown in wheat and magenta, respectively. D-Ala and ADP are drawn as CPK models. Loops II and III are predominantly involved in the formation of the D-Ala channel.
The above figures are reproduced from the cited reference with permission from the IUCr
*Note, "added" references are those not in the PDB file but which have either been obtained from the journal or suggested by the author(s).
Go to PROCHECK summary