Research workbench
Probabilistic structural models of mature P22 bacteriophage portal, hub, and tailspike proteins
Analyse Probabilistic structural models of mature P22 bacteriophage portal, hub, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GAI
- Type
- protein
- Length
- 12,390 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Portal protein; Peptidoglycan hydrolase GP4; Tail fiber protein
- EC
- 3.2.1.-
- UniProt
- P26744, P26746, P12528
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 26% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, W, X | Portal protein | protein | 721 | 44% helix, 12% strand | P26744 |
| K, L, M, N, O, P, Q, R, S, T, U, V | Peptidoglycan hydrolase GP4 | protein | 146 | 40% helix, 3% strand | P26746 |
| Y, Z, 0 | Tail fiber protein (EC 3.2.1.-) | protein | 662 | 3% helix, 36% strand | P12528 |
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 | 509 | 0.88 | 0.95 | 75 | empty |
| 2 | 1158 | 0.86 | 0.86 | 134 | empty |
| 3 | 1120 | 0.84 | 0.85 | 90 | empty |
| 4 | 893 | 0.83 | 0.85 | 91 | empty |
| 5 | 796 | 0.83 | 0.85 | 60 | empty |
Interfaces
91 interfaces between chains.
- A–B · 10205 Ų buried · 165 hydrogen bonds · protein-protein
- F–G · 10027 Ų buried · 129 hydrogen bonds · protein-protein
- B–C · 9988 Ų buried · 149 hydrogen bonds · protein-protein
- C–D · 9976 Ų buried · 139 hydrogen bonds · protein-protein
- E–F · 9866 Ų buried · 139 hydrogen bonds · protein-protein
Compared structures
- 5GAI · Probabilistic Structural Models of Mature P22 Bacteriophage Portal, Hub, and Tailspike… · the same entry in another collection · chain B against B, 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 P26744
- Every structure of UniProt P26746
- Every structure of UniProt P12528
- Elsewhere: RCSB PDB 5GAI · PDBe 5GAI · UniProt P26744 · UniProt P26746 · UniProt P12528
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