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Crystal structure of human RAB11-RABIN8-FIP3

Analyse Crystal structure of human RAB11-RABIN8-FIP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UJ3
Type: protein
Length: 2,965 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-11A; Rab-3A-interacting protein; RAB11 family-interacting protein…
UniProt: P62491, Q96QF0, O75154
Ligands: GNP, MG, SO4
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 21 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-11A	protein	176	34% helix, 28% strand	P62491
B	Rab-3A-interacting protein	protein	161	48% helix, 11% strand	Q96QF0
C	RAB11 family-interacting protein 3	protein	36	89% helix, 3% strand	O75154
D	RAS-related protein rab-11A	protein	175	34% helix, 27% strand	P62491
E	Rab-3A-interacting protein	protein	162	48% helix, 14% strand	Q96QF0
F, O, R, U	RAB11 family-interacting protein 3	protein	37	81% helix, 3% strand	O75154
G	RAS-related protein rab-11A	protein	175	34% helix, 27% strand	P62491
H	Rab-3A-interacting protein	protein	155	52% helix, 12% strand	Q96QF0
I	RAB11 family-interacting protein 3	protein	41	78% helix, 2% strand	O75154
J	RAS-related protein rab-11A	protein	174	34% helix, 27% strand	P62491
K	Rab-3A-interacting protein	protein	159	49% helix, 14% strand	Q96QF0
L	RAB11 family-interacting protein 3	protein	38	84% helix, 3% strand	O75154
M	RAS-related protein rab-11A	protein	174	34% helix, 28% strand	P62491
N	Rab-3A-interacting protein	protein	164	48% helix, 9% strand	Q96QF0
P	RAS-related protein rab-11A	protein	171	34% helix, 29% strand	P62491
Q	Rab-3A-interacting protein	protein	161	50% helix, 9% strand	Q96QF0
S	RAS-related protein rab-11A	protein	171	34% helix, 27% strand	P62491
T	Rab-3A-interacting protein	protein	164	48% helix, 8% strand	Q96QF0
V	RAS-related protein rab-11A	protein	169	34% helix, 28% strand	P62491
W	Rab-3A-interacting protein	protein	155	51% helix, 8% strand	Q96QF0
X	RAB11 family-interacting protein 3	protein	36	81% helix, 3% strand	O75154

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 8 copies · chains A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, W
MG · Magnesium ion · metal · 8 copies · chains A, D, G, J, M, P, S, V
SO4 · Sulfate ion · ion · chains M, Q
PG4 · Tetraethylene glycol · additive · chains V, W

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	789	0.73	0.78	76	SO4
2	497	0.62	0.76	59	GNP, MG
3	458	0.62	0.76	43	empty
4	346	0.59	0.77	42	GNP, MG
5	120	0.59	0.85	24	empty

Interfaces

29 interfaces between chains.

E–K · 1710 Å² buried · 26 hydrogen bonds · protein-protein
B–H · 1521 Å² buried · 21 hydrogen bonds · protein-protein
F–I · 791 Å² buried · 6 hydrogen bonds · protein-protein
V–W · 742 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 732 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4UJ3 · Crystal structure of human Rab11-Rabin8-FIP3 · the same entry in another collection · chain K against K, 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 P62491
Every structure of UniProt Q96QF0
Every structure of UniProt O75154
Elsewhere: RCSB PDB 4UJ3 · PDBe 4UJ3 · UniProt P62491 · UniProt Q96QF0 · UniProt O75154

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