SMTL ID : 7uuw.1

Cryogenic electron microscopy 3D map of F-actin bound by the Actin Binding Domain of alpha-catenin ortholog, HMP1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:L.18, A:D.159, A:D.159, A:K.215, A:G.304, A:K.338 Salt bridges: A:K.20, A:K.20 ADP.3: 15 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:L.18, B:L.18, B:D.159, B:D.159, B:K.215, B:G.304, B:K.338 Salt bridges: B:K.20, B:K.20 ADP.5: 15 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.16, C:G.17, C:L.18, C:L.18, C:D.159, C:D.159, C:K.215, C:G.304, C:K.338 Salt bridges: C:K.20, C:K.20 ADP.7: 15 residues within 4Å: Chain D: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.16, D:G.17, D:L.18, D:L.18, D:D.159, D:D.159, D:K.215, D:G.304, D:K.338 Salt bridges: D:K.20, D:K.20 ADP.9: 15 residues within 4Å: Chain E: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.16, E:G.17, E:L.18, E:L.18, E:D.159, E:D.159, E:K.215, E:G.304, E:K.338 Salt bridges: E:K.20, E:K.20 ADP.11: 15 residues within 4Å: Chain F: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.16, F:G.17, F:L.18, F:L.18, F:D.159, F:D.159, F:K.215, F:G.304, F:K.338 Salt bridges: F:K.20, F:K.20

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: Q.139 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: Q.139 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: Q.139 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: Q.139 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: Q.139 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain F: Q.139 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rangarajan, E.S. et al., The nematode alpha-catenin ortholog, HMP1, has an extended alpha-helix when bound to actin filaments. J.Biol.Chem. (2022)

Release Date

2023-01-18

Peptides

Actin, alpha skeletal muscle: ABCDEF
Alpha-catenin-like protein hmp-1: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
K

K
L

L
Z

Actin, alpha skeletal muscle

Alpha-catenin-like protein hmp-1

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