SMTL ID : 1loj.3 (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-14-mer

Ligands

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

U.1: 11 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, M.47 Ligands: URI.3, URI.13 24 PLIP interactions: 5 interactions with chain H, 1 interactions with chain B, 2 interactions with chain I, 7 interactions with chain D, 7 interactions with chain A, 1 interactions with chain N, 1 interactions with chain E Hydrogen bonds: H:N.48, H:N.48, H:R.72, H:D.74, B:R.72, I:R.72, I:R.72, D:H.46, D:N.48, D:D.74, A:N.48, A:N.48, A:R.72, A:D.74, A:D.74, N:H.46, E:R.72 pi-Stacking: H:H.46, D:H.46, A:H.46 Water bridges: D:H.46, D:N.48 Salt bridges: D:H.46, A:H.46 U.7: 11 residues within 4Å: Chain C: L.15, L.45, 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.15: 12 residues within 4Å: Chain H: H.46, N.48, R.72, G.73, D.74 Chain I: R.72 Chain N: L.15, L.45, H.46, M.47 Ligands: U.17, U.27 Protein-ligand interaction information (PLIP) not available U.17: 11 residues within 4Å: Chain H: L.45, H.46, M.47 Chain I: H.46, N.48, R.72, G.73, D.74 Chain J: R.72 Ligands: U.15, URI.19 26 PLIP interactions: 3 interactions with chain J, 6 interactions with chain N, 6 interactions with chain K, 1 interactions with chain M, 6 interactions with chain I, 2 interactions with chain H, 2 interactions with chain L Hydrogen bonds: J:R.72, J:R.72, N:N.48, N:N.48, N:R.72, N:D.74, K:H.46, K:N.48, K:N.48, K:D.74, I:N.48, I:N.48, I:R.72, I:D.74, H:R.72, L:R.72, L:R.72 Salt bridges: J:H.46, N:H.46, K:H.46, M:H.46, I:H.46, H:H.46 pi-Stacking: N:H.46, K:H.46 pi-Cation interactions: I:R.72 U.21: 11 residues within 4Å: Chain J: L.45, H.46, M.47 Chain K: H.46, N.48, R.72, G.73, D.74 Chain L: R.72 Ligands: URI.19, URI.23 Protein-ligand interaction information (PLIP) not available U.27: 11 residues within 4Å: Chain H: R.72 Chain M: L.45, H.46, M.47 Chain N: H.46, N.48, R.72, G.73, D.74 Ligands: U.15, URI.25 Protein-ligand interaction information (PLIP) not available

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

MPD.2: 7 residues within 4Å: Chain A: A.17, L.18, S.21, I.79, R.81 Chain B: T.68, L.70 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.68, B:L.70, A:A.17 Hydrogen bonds: A:S.21 Water bridges: A:R.81 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:R.81 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 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:A.17, C:L.18, C:I.79, D:V.50, D:T.68 Hydrogen bonds: C:S.21, C:R.81 Water bridges: C:R.81, C:R.81 MPD.8: 6 residues within 4Å: Chain D: A.17, L.18, S.21, I.79, R.81 Chain E: T.68 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.18 Hydrogen bonds: D:A.17 MPD.10: 8 residues within 4Å: Chain E: A.17, L.18, S.21, I.79, S.80, R.81 Chain F: V.50, T.68 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:A.17, E:I.79, F:V.50 Hydrogen bonds: E:S.21 MPD.12: 8 residues within 4Å: Chain F: A.17, S.21, I.79, S.80, R.81 Chain G: V.50, T.68, L.70 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:A.17, G:V.50 Hydrogen bonds: F:S.21, F:R.81 MPD.14: 7 residues within 4Å: Chain A: V.50, T.68 Chain G: A.17, L.18, N.20, S.21, R.81 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:A.17 MPD.16: 8 residues within 4Å: Chain H: P.14, A.17, L.18, S.21, I.79, S.80, R.81 Chain I: T.68 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:A.17 Hydrogen bonds: I:T.68 MPD.18: 7 residues within 4Å: Chain I: A.17, L.18, S.21, I.79, S.80, R.81 Chain J: T.68 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:A.17, I:I.79 Hydrogen bonds: I:S.21 MPD.20: 9 residues within 4Å: Chain J: A.17, L.18, S.21, I.79, S.80, R.81 Chain K: V.50, T.68, V.69 6 PLIP interactions: 4 interactions with chain J, 2 interactions with chain K Hydrophobic interactions: J:A.17, J:I.79, K:V.50, K:T.68 Hydrogen bonds: J:S.21 Water bridges: J:R.81 MPD.22: 7 residues within 4Å: Chain K: A.17, L.18, N.20, S.21, I.79, R.81 Chain L: T.68 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:A.17, K:L.18 Hydrophobic interactions: L:T.68 MPD.24: 11 residues within 4Å: Chain L: P.14, A.17, L.18, S.21, I.79, S.80, R.81 Chain M: V.50, T.68, V.69, L.70 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:A.17, M:V.50 Hydrogen bonds: L:S.21 MPD.26: 9 residues within 4Å: Chain M: A.17, L.18, S.21, V.26, I.79, S.80, R.81 Chain N: V.50, T.68 7 PLIP interactions: 5 interactions with chain M, 2 interactions with chain N Hydrophobic interactions: M:A.17, M:V.26, M:I.79, M:R.81, N:V.50 Water bridges: M:N.20 Hydrogen bonds: N:T.68 MPD.28: 7 residues within 4Å: Chain H: V.50, T.68 Chain N: A.17, L.18, S.21, I.79, R.81 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain H Hydrogen bonds: N:A.17, N:L.18 Hydrophobic interactions: H:V.50

8 x URI: URIDINE(Non-covalent)

URI.3: 9 residues within 4Å: Chain A: L.45, M.47 Chain B: H.46, N.48, R.72, G.73, D.74 Ligands: U.1, URI.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.46, B:N.48, B:N.48, B:R.72, B:G.73, B:D.74 pi-Stacking: B:H.46 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: URI.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:D.74, D:R.72 pi-Stacking: C:H.46 pi-Cation interactions: 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: 6 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:H.46, E:N.48, E:N.48, E:D.74, E:D.74, F:R.72, F:R.72 pi-Stacking: E:H.46 URI.11: 10 residues within 4Å: Chain E: L.45, M.47 Chain F: H.46, N.48, R.72, G.73, D.74 Chain G: R.72 Ligands: URI.9, URI.13 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:N.48, F:N.48, F:R.72, F:G.73, F:D.74, F:D.74, G:R.72, G:R.72 Water bridges: F:H.46 pi-Stacking: F:H.46 pi-Cation interactions: F:H.46 URI.13: 9 residues within 4Å: Chain F: L.45, M.47 Chain G: H.46, N.48, R.72, G.73, D.74 Ligands: U.1, URI.11 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:H.46, G:N.48, G:N.48, G:R.72, G:R.72, G:D.74, G:D.74 pi-Stacking: G:H.46 URI.19: 10 residues within 4Å: Chain I: L.45, M.47 Chain J: H.46, N.48, R.72, G.73, D.74 Chain K: R.72 Ligands: U.17, U.21 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:N.48, J:N.48, J:R.72, J:D.74, K:R.72 pi-Stacking: J:H.46 URI.23: 10 residues within 4Å: Chain K: L.45, M.47 Chain L: H.46, N.48, R.72, G.73, D.74 Chain M: R.72 Ligands: U.21, URI.25 8 PLIP interactions: 1 interactions with chain M, 7 interactions with chain L Hydrogen bonds: M:R.72, L:H.46, L:N.48, L:N.48, L:R.72, L:G.73, L:D.74 pi-Stacking: L:H.46 URI.25: 11 residues within 4Å: Chain L: L.45, M.47, D.74 Chain M: H.46, N.48, R.72, G.73, D.74 Chain N: R.72 Ligands: URI.23, U.27 6 PLIP interactions: 5 interactions with chain M, 1 interactions with chain N Hydrogen bonds: M:N.48, M:N.48, M:R.72, M:D.74, N:R.72 pi-Stacking: M: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): ABCDEFGHIJKLMN

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
J

K
K

L
L

M
M

N
N

small nuclear ribonucleoprotein homolog (Sm-like)

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