SMTL ID : 1lnx.2 (1 other biounit)

Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-14-mer

Ligands

14 x URI: URIDINE(Non-covalent)

URI.1: 11 residues within 4Å: Chain A: G.13, L.16, F.41, Q.43, V.45 Chain B: D.42, N.46 Chain N: A.10, G.13, Q.43 Ligands: URI.37 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain N Hydrophobic interactions: A:L.16 Hydrogen bonds: A:G.13 Water bridges: A:A.10, A:A.14, A:Q.17, N:G.13, N:A.14 URI.3: 11 residues within 4Å: Chain B: L.12, G.13, L.16, Q.17, F.41, D.42, Q.43, V.45 Chain M: A.10, Q.43 Ligands: URI.34 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain M Hydrophobic interactions: B:L.16 Hydrogen bonds: B:G.13, B:Q.17, M:A.10 Water bridges: B:A.10, B:A.10, B:A.14, B:F.41, M:G.13, M:G.13 URI.7: 12 residues within 4Å: Chain C: L.12, G.13, L.16, F.41, D.42, Q.43, V.45 Chain D: N.46, V.67, R.69 Chain L: Q.43 Ligands: URI.30 7 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D, 1 interactions with chain L Hydrophobic interactions: C:V.45, D:V.67 Hydrogen bonds: C:D.42, D:N.46 Water bridges: C:G.13, C:G.13, L:Q.43 URI.8: 11 residues within 4Å: Chain D: L.12, G.13, L.16, F.41, Q.43, V.45 Chain E: D.42, N.46, V.67 Chain K: Q.43 Ligands: URI.27 9 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E, 2 interactions with chain K Hydrophobic interactions: D:L.16, D:V.45, E:V.67 Water bridges: D:G.13, D:Q.17, D:Q.43 Hydrogen bonds: E:N.46, K:Q.43, K:Q.43 URI.11: 11 residues within 4Å: Chain E: G.13, L.16, Q.17, F.41, Q.43, V.45 Chain F: N.46, V.67 Chain J: Q.17, Q.43 Ligands: URI.26 7 PLIP interactions: 1 interactions with chain J, 6 interactions with chain E Hydrogen bonds: J:Q.17, E:Q.17 Hydrophobic interactions: E:L.16 Water bridges: E:A.10, E:A.10, E:G.13, E:A.14 URI.15: 10 residues within 4Å: Chain F: L.12, G.13, L.16, F.41, Q.43, V.45 Chain G: N.46, V.67 Chain I: Q.43 Ligands: URI.22 5 PLIP interactions: 2 interactions with chain I, 2 interactions with chain F, 1 interactions with chain G Water bridges: I:Q.43, I:Q.43, F:G.13 Hydrophobic interactions: F:V.45, G:V.67 URI.18: 12 residues within 4Å: Chain A: D.42, N.46, V.67 Chain G: L.12, G.13, L.16, F.41, D.42, Q.43, V.45 Chain H: Q.43 Ligands: URI.20 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: G:V.45, A:V.67 Hydrogen bonds: G:L.12, G:Q.17, A:D.42, A:N.46 URI.20: 11 residues within 4Å: Chain G: A.10, G.13, Q.43 Chain H: G.13, L.16, F.41, Q.43, V.45 Chain I: D.42, N.46 Ligands: URI.18 8 PLIP interactions: 2 interactions with chain G, 5 interactions with chain H, 1 interactions with chain I Water bridges: G:G.13, G:A.14, H:A.10, H:A.14, H:Q.17 Hydrophobic interactions: H:L.16 Hydrogen bonds: H:G.13, I:D.42 URI.22: 11 residues within 4Å: Chain F: A.10, Q.43 Chain I: L.12, G.13, L.16, Q.17, F.41, D.42, Q.43, V.45 Ligands: URI.15 12 PLIP interactions: 7 interactions with chain I, 2 interactions with chain J, 3 interactions with chain F Hydrophobic interactions: I:L.16 Hydrogen bonds: I:G.13, I:Q.17, F:A.10 Water bridges: I:A.10, I:A.10, I:A.14, I:F.41, J:D.42, J:D.42, F:G.13, F:G.13 URI.26: 12 residues within 4Å: Chain E: Q.43 Chain J: L.12, G.13, L.16, F.41, D.42, Q.43, V.45 Chain K: N.46, V.67, R.69 Ligands: URI.11 8 PLIP interactions: 3 interactions with chain K, 4 interactions with chain J, 1 interactions with chain E Hydrophobic interactions: K:V.67, J:V.45 Hydrogen bonds: K:N.46, J:D.42 Water bridges: K:D.42, J:G.13, J:G.13, E:Q.43 URI.27: 11 residues within 4Å: Chain D: Q.43 Chain K: L.12, G.13, L.16, F.41, Q.43, V.45 Chain L: D.42, N.46, V.67 Ligands: URI.8 10 PLIP interactions: 2 interactions with chain D, 3 interactions with chain L, 5 interactions with chain K Hydrogen bonds: D:Q.43, D:Q.43, L:D.42, L:N.46 Hydrophobic interactions: L:V.67, K:L.16, K:V.45 Water bridges: K:G.13, K:Q.17, K:Q.43 URI.30: 11 residues within 4Å: Chain C: Q.17, Q.43 Chain L: G.13, L.16, Q.17, F.41, Q.43, V.45 Chain M: N.46, V.67 Ligands: URI.7 9 PLIP interactions: 1 interactions with chain C, 6 interactions with chain L, 2 interactions with chain M Hydrogen bonds: C:Q.17, L:Q.17 Hydrophobic interactions: L:L.16 Water bridges: L:A.10, L:A.10, L:G.13, L:A.14, M:D.42, M:D.42 URI.34: 10 residues within 4Å: Chain B: Q.43 Chain M: L.12, G.13, L.16, F.41, Q.43, V.45 Chain N: N.46, V.67 Ligands: URI.3 6 PLIP interactions: 2 interactions with chain N, 2 interactions with chain M, 2 interactions with chain B Hydrophobic interactions: N:V.67, M:V.45 Hydrogen bonds: N:D.42 Water bridges: M:G.13, B:Q.43, B:Q.43 URI.37: 12 residues within 4Å: Chain A: Q.43 Chain H: D.42, N.46, V.67 Chain N: L.12, G.13, L.16, F.41, D.42, Q.43, V.45 Ligands: URI.1 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain N Hydrophobic interactions: H:V.67, N:V.45 Hydrogen bonds: H:D.42, H:D.42, H:N.46, N:L.12, N:Q.17

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: K.27, E.33, I.55 Chain B: E.54, I.56, Y.61, R.63 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain B: K.27, E.33, I.55 Chain C: E.54, I.56, R.63 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain C: K.27, E.33 Chain D: E.54, I.56, Y.61, R.63 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain D: K.27, E.33 Chain E: I.56, Y.61, R.63 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain E: K.27, E.33 Chain F: I.56, Y.61, R.63 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain E: R.35, I.55, G.58, V.60 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain E: Q.23, R.35, G.36, I.37, D.51 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain F: N.59, V.60, Y.61 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain F: K.27, E.33 Chain G: E.54, Y.61, R.63 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain A: E.54, I.56, Y.61, R.63 Chain G: K.27, E.33, I.55 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain H: K.27, E.33, I.55 Chain I: E.54, I.56, Y.61, R.63 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain I: K.27, E.33, I.55 Chain J: E.54, I.56, R.63 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain J: K.27, E.33 Chain K: E.54, I.56, Y.61, R.63 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain K: K.27, E.33 Chain L: I.56, Y.61, R.63 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain L: K.27, E.33 Chain M: I.56, Y.61, R.63 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain L: R.35, I.55, G.58, V.60 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain L: Q.23, R.35, G.36, I.37, D.51 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain M: N.59, V.60, Y.61 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain M: K.27, E.33 Chain N: E.54, Y.61, R.63 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain H: E.54, I.56, Y.61, R.63 Chain N: K.27, E.33, I.55 Ligand excluded by PLIP

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

ACY.5: 7 residues within 4Å: Chain A: R.29 Chain B: R.29 Chain C: R.29 Chain D: R.29 Chain E: R.29 Chain F: R.29 Chain G: R.29 7 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain G, 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain F Salt bridges: D:R.29, B:R.29, G:R.29, A:R.29, C:R.29, E:R.29, F:R.29 ACY.9: 3 residues within 4Å: Chain D: R.35, I.55, G.58 No protein-ligand interaction detected (PLIP) ACY.24: 7 residues within 4Å: Chain H: R.29 Chain I: R.29 Chain J: R.29 Chain K: R.29 Chain L: R.29 Chain M: R.29 Chain N: R.29 7 PLIP interactions: 1 interactions with chain M, 1 interactions with chain J, 1 interactions with chain I, 1 interactions with chain N, 1 interactions with chain H, 1 interactions with chain K, 1 interactions with chain L Salt bridges: M:R.29, J:R.29, I:R.29, N:R.29, H:R.29, K:R.29, L:R.29 ACY.28: 3 residues within 4Å: Chain K: R.35, I.55, G.58 No protein-ligand interaction detected (PLIP)

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
A

I
B

J
C

K
D

L
E

M
F

N
G

small nuclear ribonucleoprotein homolog (Sm-like)

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