SMTL ID : 1loj.2 (2 other biounits)

Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-heptamer

Ligands

4 x U: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U.1: 12 residues within 4Å: Chain A: H.46, N.48, R.72, G.73, D.74 Chain B: R.72 Chain G: L.15, L.45, H.46, M.47 Ligands: U.3, U.13 33 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A, 1 interactions with chain F, 3 interactions with chain C, 6 interactions with chain D, 2 interactions with chain E, 7 interactions with chain G Hydrogen bonds: B:N.48, B:N.48, B:R.72, B:R.72, B:D.74, A:N.48, A:N.48, A:R.72, A:R.72, A:D.74, C:R.72, C:R.72, D:H.46, D:N.48, D:N.48, D:D.74, E:R.72, E:R.72, G:H.46, G:N.48, G:N.48, G:R.72, G:D.74 Salt bridges: B:H.46, A:H.46, F:H.46, C:H.46, D:H.46, G:H.46 pi-Cation interactions: B:R.72 pi-Stacking: A:H.46, D:H.46, G:H.46 U.3: 11 residues within 4Å: Chain A: L.45, H.46, M.47 Chain B: H.46, N.48, R.72, G.73, D.74 Chain C: R.72 Ligands: U.1, URI.5 Protein-ligand interaction information (PLIP) not available U.7: 11 residues within 4Å: Chain C: L.45, H.46, M.47 Chain D: H.46, N.48, R.72, G.73, D.74 Chain E: R.72 Ligands: URI.5, URI.9 Protein-ligand interaction information (PLIP) not available U.13: 11 residues within 4Å: Chain A: R.72 Chain F: L.45, H.46, M.47 Chain G: H.46, N.48, R.72, G.73, D.74 Ligands: U.1, URI.11 Protein-ligand interaction information (PLIP) not available

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 8 residues within 4Å: Chain A: P.14, A.17, L.18, S.21, I.79, S.80, R.81 Chain B: T.68 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.68 Hydrophobic interactions: A:A.17 MPD.4: 7 residues within 4Å: Chain B: A.17, L.18, S.21, I.79, S.80, R.81 Chain C: T.68 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.17, B:I.79 Hydrogen bonds: B:S.21 MPD.6: 9 residues within 4Å: Chain C: A.17, L.18, S.21, I.79, S.80, R.81 Chain D: V.50, T.68, V.69 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:V.50, D:T.68, C:A.17, C:I.79 Hydrogen bonds: C:S.21 Water bridges: C:R.81 MPD.8: 7 residues within 4Å: Chain D: A.17, L.18, N.20, S.21, I.79, R.81 Chain E: T.68 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:A.17, D:L.18 Hydrophobic interactions: E:T.68 MPD.10: 11 residues within 4Å: Chain E: P.14, A.17, L.18, S.21, I.79, S.80, R.81 Chain F: V.50, T.68, V.69, L.70 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:A.17, F:V.50 Hydrogen bonds: E:S.21 MPD.12: 9 residues within 4Å: Chain F: A.17, L.18, S.21, V.26, I.79, S.80, R.81 Chain G: V.50, T.68 7 PLIP interactions: 2 interactions with chain G, 5 interactions with chain F Hydrophobic interactions: G:V.50, F:A.17, F:V.26, F:I.79, F:R.81 Hydrogen bonds: G:T.68 Water bridges: F:N.20 MPD.14: 7 residues within 4Å: Chain A: V.50, T.68 Chain G: A.17, L.18, S.21, I.79, R.81 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:V.50 Hydrogen bonds: G:A.17, G:L.18

3 x URI: URIDINE(Non-covalent)

URI.5: 10 residues within 4Å: Chain B: L.45, M.47 Chain C: H.46, N.48, R.72, G.73, D.74 Chain D: R.72 Ligands: U.3, U.7 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.48, C:N.48, C:R.72, C:D.74, D:R.72 pi-Stacking: C:H.46 URI.9: 10 residues within 4Å: Chain D: L.45, M.47 Chain E: H.46, N.48, R.72, G.73, D.74 Chain F: R.72 Ligands: U.7, URI.11 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:H.46, E:N.48, E:N.48, E:R.72, E:G.73, E:D.74, F:R.72 pi-Stacking: E:H.46 URI.11: 11 residues within 4Å: Chain E: L.45, M.47, D.74 Chain F: H.46, N.48, R.72, G.73, D.74 Chain G: R.72 Ligands: URI.9, U.13 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:N.48, F:N.48, F:R.72, F:D.74, G:R.72 pi-Stacking: F:H.46

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

small nuclear ribonucleoprotein homolog (Sm-like): ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

E
L

F
M

G
N

small nuclear ribonucleoprotein homolog (Sm-like)

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