MolNFT v1 · #137051 · protein
Crystal structure of holo-(acyl-carrier-protein) SYNTHASE:HOLO(ACYL- carrier-protein) complex from escherichia COLI.
5VCB · Holo-[acyl-carrier-protein] synthase: “Crystal structure of holo-(acyl-carrier-protein) SYNTHASE:HOLO(ACYL- carrier-protein) complex from…”. X-ray diffraction, 1 ligand (PNS), 20 pockets (best druggability 0.90). MolNFT v1 #137051…
- PDB
- 5VCB
- Type
- protein
- Length
- 2,970 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holo-[acyl-carrier-protein] synthase; Acyl carrier protein
- EC
- 2.7.8.7
- UniProt
- P24224, B7MJ81
- Ligands
- PNS
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| b, G, O, T | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 121 | 47% helix, 31% strand | P24224 |
| a, I, N, A, S | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 122 | 46% helix, 30% strand | P24224 |
| c, H, U | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 120 | 44% helix, 31% strand | P24224 |
| f, e, d, K, J, L, F, E, D, P, R, Q, X, W, V | Acyl carrier protein | protein | 77 | 58% helix, 3% strand | B7MJ81 |
| M | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 123 | 43% helix, 30% strand | P24224 |
| B, C | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 119 | 48% helix, 31% strand | P24224 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · 14 copies · chains a, c, f, b, e, d, G, H, J, I, L, F, A, C, E, B, D, N, M, P, O, R, Q, S, U, X, T, W, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.90 | 0.91 | 147 | PNS |
| 2 | 959 | 0.89 | 0.90 | 140 | PNS |
| 3 | 933 | 0.89 | 0.91 | 122 | PNS |
| 4 | 856 | 0.88 | 0.90 | 114 | PNS |
| 5 | 675 | 0.81 | 0.85 | 63 | PNS |
Interfaces
58 interfaces between chains.
- b–a · 789 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 770 Ų buried · 11 hydrogen bonds · protein-protein
- T–S · 742 Ų buried · 9 hydrogen bonds · protein-protein
- O–N · 742 Ų buried · 4 hydrogen bonds · protein-protein
- I–H · 739 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 cofactor (phosphopantetheinylation).
Compared structures
- 5VCB · Crystal structure of holo-(acyl-carrier-protein) synthase:holo(acyl-carrier-protein)… · the same entry in another collection · chain J against J, 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 P24224
- Every structure of UniProt B7MJ81
- Elsewhere: RCSB PDB 5VCB · PDBe 5VCB · UniProt P24224 · UniProt B7MJ81
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