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An activated, truncated gamma-delta resolvase tetramer

Analyse An activated, truncated gamma-delta resolvase tetramer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GM5
Type: protein
Length: 469 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transposon gamma-delta resolvase
UniProt: P03012
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 54% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transposon gamma-delta resolvase	protein	122	55% helix, 18% strand	P03012
B	Transposon gamma-delta resolvase	protein	114	51% helix, 19% strand	P03012
C	Transposon gamma-delta resolvase	protein	116	53% helix, 17% strand	P03012
D	Transposon gamma-delta resolvase	protein	117	56% helix, 17% strand	P03012

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	235	0.60	0.80	25	empty
2	115	0.55	0.83	16	empty
3	96	0.53	0.84	17	empty
4	157	0.48	0.77	24	empty
5	83	0.34	0.75	14	empty

Interfaces

6 interfaces between chains.

C–D · 806 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 611 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 552 Å² buried · 1 hydrogen bond · protein-protein
A–D · 469 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 402 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

2GM5 · An activated, truncated gamma-delta resolvase tetramer · the same entry in another collection · chain C against C, TM-score 1.00
P03012 · AlphaFold monomer V2.0 prediction for transposon gamma-delta resolvase (P03012) · 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 P03012
Elsewhere: RCSB PDB 2GM5 · PDBe 2GM5 · UniProt P03012

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