5DPW: PLEKHM1 LIR

Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125. Determined by X-ray diffraction at 2.19 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 16
Atoms: 8,460
Mol. weight: 124.44 kDa
Released: 28 Sept 2016

Explore 5DPW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DPW contains 39 α-helices and 70 β-strands across 16 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	9-22	14
β-strand	27-33	7	1
α-helix	41-43	3
β-strand	47-50	4	1
β-strand	55	1	2
α-helix	56-65	10
β-strand	76-79	4	1
β-strand	83-84	2	1
β-strand	90	1	2
α-helix	91-98	8
β-strand	105-110	6	1
β-strand	113-114	2	3

Chains B, D, F and P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-8	3	1

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	9-22	14
β-strand	27-33	7	4
α-helix	41-43	3
β-strand	47-50	4	4
β-strand	55	1	5
α-helix	56-65	10
β-strand	76-79	4	4
β-strand	83-84	2	4
β-strand	90	1	5
α-helix	91-98	8
α-helix	104	1
β-strand	105-110	6	4
β-strand	113-114	2	6

Chain E: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	9-22	14
β-strand	26-33	8	3
α-helix	41-43	3
β-strand	47-51	5	3
β-strand	55	1	7
α-helix	56-64	9
β-strand	76-79	4	3
β-strand	83-84	2	3
β-strand	90	1	7
α-helix	91-98	8
β-strand	105-110	6	3
β-strand	113-114	2	1

Chain G: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	9-20	12
β-strand	26-33	8	6
α-helix	41-43	3
β-strand	47-51	5	6
β-strand	55	1	8
α-helix	56-64	9
β-strand	76-79	4	6
β-strand	83-84	2	6
β-strand	90	1	8
α-helix	91-98	8
β-strand	105-110	6	6
β-strand	113-114	2	4

Chains H, J, L and N: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7-8	2	6

Chain I: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	9-22	14
β-strand	27-33	7	9
β-strand	47-50	4	9
β-strand	55	1	10
α-helix	56-66	11
β-strand	76-79	4	9
β-strand	83-84	2	9
β-strand	90	1	10
α-helix	91-98	8
β-strand	105-110	6	9
β-strand	113-114	2	11

Chain K: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	9-22	14
β-strand	27-33	7	12
α-helix	41-43	3
β-strand	47-50	4	12
β-strand	55	1	13
α-helix	56-66	11
β-strand	76-79	4	12
β-strand	83	1	12
β-strand	90	1	13
α-helix	91-98	8
β-strand	105-110	6	12

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Microtubule-associated proteins 1A/1B light chain 3C	A, C, E, G, I, K, M, O	protein	118	Homo sapiens	Q9BXW4 (AlphaFold model)
Pleckstrin homology domain-containing family M member 1	B, D, F, H, J, L, N, P	protein	14	Homo sapiens	Q9Y4G2 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA

>5DPW_1 Microtubule-associated proteins 1A/1B light chain 3C (chains A, C, E, G, I, K, M, O)
PSVRPFKQRKSLAIRQEEVAGIRAKFPNKIPVVVERYPRETFLPPLDKTKFLVPQELTMT
QFLSIIRSRMVLRATEAFYLLVNNKSLVSMSATMAEIYRDYKDEDGFVYMTYASQETF

Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA

>5DPW_2 Pleckstrin homology domain-containing family M member 1 (chains B, D, F, H, J, L, N, P)
PQQEDEWVNVQYPD

Primary citation

Structural and functional analysis of the GABARAP interaction motif (GIM). Rogov, V.V., Stolz, A., Ravichandran, A.C. et al. EMBO Rep (2017) 18:1382-1396. DOI 10.15252/embr.201643587 · PubMed

Other PDB entries of the same protein (UniProt Q9BXW4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WAM 1.75 Å, Crystal structure of human LC3C_8-125
3VVW 2.5 Å, NDP52 in complex with LC3C
3WAP 3.1 Å, Crystal structure of Atg13 LIR-fused human LC3C_8-125
2NCN Solution Structure of the Autophagy-Related Protein LC3C

Browse structure collections

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