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Crystal structure of AMP-pnp complexed D-alanine-D-alanine LIGASE(DDL) from yersinia pestis
Analyse Crystal structure of AMP-pnp complexed D-alanine-D-alanine LIGASE(DDL) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C1O
- Type
- protein
- Length
- 1,188 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- Q8ZIE7
- Ligands
- ANP, NA, MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 297 | 35% helix, 23% strand | Q8ZIE7 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 290 | 37% helix, 24% strand | Q8ZIE7 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 306 | 38% helix, 22% strand | Q8ZIE7 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 295 | 37% helix, 23% strand | Q8ZIE7 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.80 | 0.85 | 78 | ANP, MG |
| 2 | 1114 | 0.77 | 0.79 | 89 | ANP, MG |
| 3 | 1036 | 0.74 | 0.77 | 96 | ANP, MG |
| 4 | 861 | 0.71 | 0.76 | 86 | ANP |
| 5 | 469 | 0.61 | 0.75 | 58 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1087 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1030 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 490 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5C1O · Crystal structure of AMP-PNP complexed D-alanine-D-alanine ligase(DDL) from Yersinia… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8ZIE7 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q8ZIE7) · a predicted model of the same protein · chain D against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8ZIE7
- Elsewhere: RCSB PDB 5C1O · PDBe 5C1O · UniProt Q8ZIE7
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