SMTL ID : 1jbm.1

Heptameric crystal structure of Mth649, an Sm-like archaeal protein from Methanobacterium thermautotrophicum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-heptamer

Ligands

5 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 7 residues within 4Å: Chain A: A.17, L.18, S.21, I.79, S.80 Chain B: T.68, L.70 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.70, A:A.17, A:L.18 Hydrogen bonds: A:S.21 ACY.4: 7 residues within 4Å: Chain C: A.17, L.18, S.21, I.79, S.80, R.81 Chain D: T.68 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.17 Hydrogen bonds: C:S.21 Water bridges: C:R.81 ACY.7: 4 residues within 4Å: Chain D: K.31, G.32, D.33 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.32, D:D.33 ACY.10: 7 residues within 4Å: Chain E: K.31, G.32, D.33 Chain F: K.31, G.32, R.34 Ligands: EDO.12 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Salt bridges: F:R.34 Hydrophobic interactions: E:K.31 Hydrogen bonds: E:D.33 Water bridges: E:D.33 ACY.14: 4 residues within 4Å: Chain F: Q.12, R.13 Chain G: S.42, F.43 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:Q.12 Water bridges: F:R.13 Salt bridges: F:R.13 Hydrophobic interactions: G:F.43

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain C: V.39, K.41, N.52, D.53 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.41, C:K.41, C:N.52, C:D.53, C:D.53 EDO.3: 6 residues within 4Å: Chain B: L.45, H.46, M.47 Chain C: H.46, N.48, R.72 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.48, C:R.72, C:R.72 Water bridges: C:H.46 EDO.5: 5 residues within 4Å: Chain C: V.11, Q.12 Chain D: F.43, D.44, L.45 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.44 EDO.6: 6 residues within 4Å: Chain C: K.31, V.77 Chain D: L.30, K.31, R.34, N.75 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.34, D:R.34 EDO.8: 2 residues within 4Å: Chain E: L.22, N.23 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.22, E:N.23 EDO.9: 6 residues within 4Å: Chain D: K.31, V.77 Chain E: L.30, K.31, N.75 Ligands: ACY.7 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Water bridges: E:K.31, D:K.31 EDO.11: 4 residues within 4Å: Chain F: V.39, K.41, N.52, D.53 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.41, F:N.52 EDO.12: 5 residues within 4Å: Chain E: K.29, V.77 Chain F: R.34, E.56 Ligands: ACY.10 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.34, F:E.56 Water bridges: E:K.29 EDO.13: 4 residues within 4Å: Chain F: L.18, S.21, I.79 Chain G: T.68 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.21, F:I.79 EDO.15: 3 residues within 4Å: Chain F: L.45 Chain G: H.46 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.45 EDO.16: 6 residues within 4Å: Chain F: L.45, H.46 Chain G: H.46, N.48, R.72 Ligands: EDO.15 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:H.46, G:N.48, G:R.72, G:R.72 Water bridges: G:G.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mura, C. et al., The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs). Protein Sci. (2003)

Release Date

2003-03-25

Peptides

PUTATIVE SNRNP SM-LIKE PROTEIN: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

PUTATIVE SNRNP SM-LIKE PROTEIN