MolNFT v1 · #164998 · protein
Structure of the PBP/SBP mota in complex with mannopinic acid from A.TUMEFACIEN R10
6TG2: “Structure of the PBP/SBP mota in complex with mannopinic acid from A.TUMEFACIEN R10”. X-ray diffraction, 2 ligands (N72, CA), 17 pockets (best druggability 0.80). MolNFT v1 #164998 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6TG2
- Type
- protein
- Length
- 1,300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mota
- UniProt
- Q44384
- Ligands
- N72, CA
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mota | protein | 326 | 46% helix, 20% strand | Q44384 |
| B | Mota | protein | 325 | 45% helix, 20% strand | Q44384 |
| C | Mota | protein | 326 | 45% helix, 20% strand | Q44384 |
| D | Mota | protein | 323 | 45% helix, 20% strand | Q44384 |
Ligands and binding sites
- N72 · (2~{R})-2-[[(3~{R},4~{R},5~{S})-3,4,5,6-tetrakis(oxidanyl)-2-oxidanylidene-hexyl]amino]pentanedioic acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 5 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.80 | 0.97 | 32 | N72 |
| 2 | 152 | 0.80 | 0.96 | 40 | N72 |
| 3 | 160 | 0.79 | 0.96 | 41 | N72 |
| 4 | 140 | 0.79 | 0.96 | 33 | N72 |
| 5 | 795 | 0.70 | 0.76 | 69 | CA |
Interfaces
4 interfaces between chains.
- A–B · 526 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 513 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 469 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6TG2 · Structure of the PBP/SBP MotA in complex with mannopinic acid from A.tumefacien R10 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q44384
- Elsewhere: RCSB PDB 6TG2 · PDBe 6TG2 · UniProt Q44384
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