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Crystal structure of MYO5B globular tail domain in complex with inactive RAB11A

Analyse Crystal structure of MYO5B globular tail domain in complex with inactive RAB11A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LWZ
Type: protein
Length: 1,030 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-11A; Unconventional myosin-vb
UniProt: P62491, Q9ULV0
Ligands: GDP, MG
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 54% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-11A	protein	162	36% helix, 28% strand	P62491
B	Unconventional myosin-vb	protein	367	62% helix, 1% strand	Q9ULV0
C	RAS-related protein rab-11A	protein	155	35% helix, 27% strand	P62491
D	Unconventional myosin-vb	protein	346	61% helix, 1% strand	Q9ULV0

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	893	0.73	0.77	110	GDP, MG
2	789	0.70	0.77	86	GDP, MG
3	449	0.69	0.80	51	empty
4	91	0.63	0.89	24	empty
5	219	0.53	0.77	33	empty

Interfaces

5 interfaces between chains.

A–B · 695 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 630 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 547 Å² buried · 1 hydrogen bond · protein-protein
B–C · 546 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 27 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4LWZ · Crystal structure of Myo5b globular tail domain in complex with inactive Rab11a · the same entry in another collection · chain D against D, TM-score 1.00
P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain C against A, TM-score 0.98
Q9ULV0 · AlphaFold monomer V2.0 prediction for unconventional myosin-vb (Q9ULV0) · a predicted model of the same protein · chain B 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 P62491
Every structure of UniProt Q9ULV0
Elsewhere: RCSB PDB 4LWZ · PDBe 4LWZ · UniProt P62491 · UniProt Q9ULV0

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