MolNFT v1 · #126737 · protein
Cryo-EM structure of lambda phage protein gams bound to recbcd.
5MBV · Recbcd enzyme subunit recb: “Cryo-EM structure of lambda phage protein gams bound to recbcd.”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #126737 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MBV
- Type
- protein
- Length
- 3,014 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recbcd enzyme subunit recb; Recbcd enzyme subunit recc; Recbcd enzyme subunit recd…
- EC
- 3.1.11.5
- UniProt
- P08394, P07648, P04993, P03702
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Recbcd enzyme subunit recb (EC 3.1.11.5) | protein | 1127 | 50% helix, 13% strand | P08394 |
| C | Recbcd enzyme subunit recc (EC 3.1.11.5) | protein | 1121 | 48% helix, 12% strand | P07648 |
| D | Recbcd enzyme subunit recd (EC 3.1.11.5) | protein | 593 | 43% helix, 15% strand | P04993 |
| A | Host-nuclease inhibitor protein gam | protein | 98 | 85% helix, 0% strand | P03702 |
| E | Host-nuclease inhibitor protein gam | protein | 75 | 85% helix, 0% strand | P03702 |
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 | 635 | 0.83 | 0.88 | 76 | empty |
| 2 | 1072 | 0.81 | 0.82 | 111 | empty |
| 3 | 1039 | 0.79 | 0.81 | 109 | empty |
| 4 | 1154 | 0.79 | 0.81 | 104 | empty |
| 5 | 860 | 0.77 | 0.80 | 77 | empty |
Interfaces
8 interfaces between chains.
- B–C · 7667 Ų buried · 78 hydrogen bonds · protein-protein
- A–E · 1767 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 1633 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1466 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 569 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5MBV · Cryo-EM structure of Lambda Phage protein GamS bound to RecBCD. · the same entry in another collection · chain E against E, TM-score 1.00
- P07648 · AlphaFold monomer V2.0 prediction for recbcd enzyme subunit recc (P07648) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P04993 · AlphaFold monomer V2.0 prediction for recbcd enzyme subunit recd (P04993) · a predicted model of the same protein · chain D against A, TM-score 0.93
- P08394 · AlphaFold monomer V2.0 prediction for recbcd enzyme subunit recb (P08394) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 P08394
- Every structure of UniProt P07648
- Every structure of UniProt P04993
- Every structure of UniProt P03702
- Elsewhere: RCSB PDB 5MBV · PDBe 5MBV · UniProt P08394 · UniProt P07648 · UniProt P04993 · UniProt P03702
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