SMTL ID : 3klt.1 (2 other biounits)

Crystal structure of a vimentin fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.1: 11 residues within 4Å: Chain A: Y.14, A.18, N.21, E.24, A.25 Chain C: N.21, E.24, A.25, W.28, Y.29 Ligands: PG4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.21, A:E.24, A:E.24

3 x SM: SAMARIUM (III) ION(Non-functional Binders)(Non-covalent)

SM.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SM.4: 3 residues within 4Å: Chain D: E.24 Ligands: 1PE.10, PGE.11 No protein-ligand interaction detected (PLIP) SM.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 10 residues within 4Å: Chain B: Y.14, V.17, A.18, N.21 Chain D: N.21, A.25, W.28, Y.29 Ligands: PG4.7, 1PE.10 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.13: 1 residues within 4Å: Chain D: E.53 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain D: K.32 No protein-ligand interaction detected (PLIP) CA.15: 1 residues within 4Å: Chain D: D.35 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 11 residues within 4Å: Chain A: E.24, A.25, Y.29 Chain C: Y.14, V.17, A.18, N.21, L.22, A.25 Ligands: P33.1, P6G.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24, A:Y.29 PG4.8: 6 residues within 4Å: Chain A: Y.29 Chain B: Y.29, F.33 Chain C: R.11, Y.14, E.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.11, C:E.15

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.10: 10 residues within 4Å: Chain B: E.24, A.25, W.28, Y.29 Chain D: Y.14, V.17, A.18, N.21 Ligands: P6G.3, SM.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.21

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 3 residues within 4Å: Chain D: E.24, W.28 Ligands: SM.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolet, S. et al., Atomic structure of vimentin coil 2. J.Struct.Biol. (2010)

Release Date

2010-05-26

Peptides

Vimentin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Vimentin

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