SMTL ID : 1m5q.2 (1 other biounit)

Crystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-14-mer

Ligands

14 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: E.73 Chain G: H.28 4 PLIP interactions: 1 interactions with chain G, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: G:H.28, A:E.73, A:E.73, H2O.15 CD.2: 2 residues within 4Å: Chain A: H.28 Chain B: E.73 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.73, A:H.28, H2O.1, H2O.3, H2O.5 CD.3: 2 residues within 4Å: Chain B: H.28 Chain C: E.73 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:E.73, C:E.73, B:H.28, H2O.4, H2O.6 CD.4: 2 residues within 4Å: Chain C: H.28 Chain D: E.73 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:E.73, D:E.73, C:H.28, H2O.6, H2O.9 CD.5: 2 residues within 4Å: Chain D: H.28 Chain E: E.73 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: D:H.28, E:E.73, E:E.73, H2O.8, H2O.10 CD.8: 2 residues within 4Å: Chain E: H.28 Chain F: E.73 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: F:E.73, E:H.28, H2O.11, H2O.11, H2O.14 CD.10: 2 residues within 4Å: Chain F: H.28 Chain G: E.73 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: F:H.28, G:E.73, H2O.12, H2O.13, H2O.16 CD.11: 1 residues within 4Å: Chain H: H.28 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:H.28, H2O.18, H2O.18, H2O.21, H2O.22 CD.15: 1 residues within 4Å: Chain I: H.28 5 PLIP interactions: 1 interactions with chain I, 4 Ligand-Water interactions Metal complexes: I:H.28, H2O.23, H2O.23, H2O.24, H2O.24 CD.19: 1 residues within 4Å: Chain J: H.28 4 PLIP interactions: 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:H.28, H2O.26, H2O.28, H2O.28 CD.22: 2 residues within 4Å: Chain K: H.28 Chain L: E.4 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: L:E.4, L:E.4, K:H.28, H2O.31, H2O.34 CD.24: 1 residues within 4Å: Chain L: H.28 4 PLIP interactions: 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:H.28, H2O.32, H2O.33, H2O.33 CD.26: 2 residues within 4Å: Chain M: H.28 Chain N: E.4 3 PLIP interactions: 1 interactions with chain N, 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: N:E.4, M:H.28, H2O.9 CD.29: 2 residues within 4Å: Chain H: E.4 Chain N: H.28 4 PLIP interactions: 1 interactions with chain N, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: N:H.28, H:E.4, H2O.6, H2O.38

3 x NA: SODIUM ION(Non-functional Binders)

NA.6: 1 residues within 4Å: Chain C: E.47 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.47 NA.9: 1 residues within 4Å: Chain D: E.47 No protein-ligand interaction detected (PLIP) NA.12: 2 residues within 4Å: Chain H: E.21, E.47 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:E.21

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain D: E.79, P.83, G.84 Chain M: N.50, R.51 Chain N: R.68, E.105, I.106 7 PLIP interactions: 4 interactions with chain M, 1 interactions with chain D, 2 interactions with chain N Hydrogen bonds: M:N.50, M:R.51, D:G.84, N:R.68, N:R.68 Water bridges: M:H.28, M:N.40 GOL.13: 8 residues within 4Å: Chain B: E.79, P.83, G.84 Chain H: H.28, N.50, R.51 Chain I: R.68, E.105 8 PLIP interactions: 3 interactions with chain H, 3 interactions with chain B, 2 interactions with chain I Hydrogen bonds: H:N.50, B:E.79, I:R.68, I:E.105 Water bridges: H:N.40, H:R.51, B:G.84, B:G.84 GOL.16: 6 residues within 4Å: Chain I: E.21, E.47, F.49 Chain J: Q.14, V.22, K.44 6 PLIP interactions: 2 interactions with chain J, 4 interactions with chain I Hydrogen bonds: J:K.44, I:E.21, I:Y.23, I:Y.23, I:N.43 Water bridges: J:Q.14 GOL.20: 9 residues within 4Å: Chain A: E.79, G.84 Chain I: H.28, A.39, N.50, R.51 Chain J: R.68, E.105, I.106 8 PLIP interactions: 5 interactions with chain I, 2 interactions with chain J, 1 interactions with chain A Hydrogen bonds: I:H.28, I:N.50, I:R.51, J:R.68, J:R.68, A:G.84 Water bridges: I:N.40, I:N.40 GOL.27: 8 residues within 4Å: Chain M: E.21, Y.23, E.47, F.49 Chain N: Q.14, V.16, V.22, K.44 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:E.21, N:Q.14, N:K.44 GOL.30: 7 residues within 4Å: Chain H: Q.14, V.16, V.22, K.44 Chain N: E.21, E.47, F.49 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain N Hydrogen bonds: H:Q.14, N:E.21

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

ACY.14: 8 residues within 4Å: Chain C: F.82, P.113, V.114, R.117 Chain H: I.89, T.92, V.94, R.102 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain C Hydrophobic interactions: H:I.89, C:P.113, C:V.114 Hydrogen bonds: H:T.92, H:T.92 Salt bridges: H:R.102 ACY.17: 8 residues within 4Å: Chain B: F.82, P.113, V.114, R.117 Chain I: I.89, T.92, V.94, R.102 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain I Hydrophobic interactions: B:P.113, B:V.114, I:I.89 Hydrogen bonds: I:T.92 Salt bridges: I:R.102 ACY.18: 6 residues within 4Å: Chain I: L.8, R.11, E.12, S.64, T.65, E.66 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain I Water bridges: H:R.51 Hydrophobic interactions: I:E.66 Hydrogen bonds: I:T.65, I:T.65, I:E.66 Salt bridges: I:R.11 ACY.21: 8 residues within 4Å: Chain A: F.82, P.113, V.114, R.117 Chain J: I.89, T.92, V.94, R.102 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain A Hydrophobic interactions: J:I.89, A:P.113, A:V.114 Hydrogen bonds: J:T.92 Salt bridges: J:R.102 ACY.23: 8 residues within 4Å: Chain G: F.82, P.113, V.114, R.117 Chain K: I.89, T.92, V.94, R.102 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain G Hydrophobic interactions: K:I.89, G:P.113, G:V.114 Salt bridges: K:R.102 Hydrogen bonds: G:P.113 ACY.25: 8 residues within 4Å: Chain F: F.82, P.113, V.114, R.117 Chain L: I.89, T.92, V.94, R.102 7 PLIP interactions: 4 interactions with chain L, 3 interactions with chain F Hydrophobic interactions: L:I.89, L:V.94, F:P.113, F:V.114 Hydrogen bonds: L:T.92, F:P.113 Salt bridges: L:R.102 ACY.28: 9 residues within 4Å: Chain E: F.82, P.113, V.114, R.117 Chain M: I.89, T.92, V.94, L.96, R.102 7 PLIP interactions: 6 interactions with chain M, 1 interactions with chain E Hydrophobic interactions: M:I.89, M:V.94, M:L.96, E:P.113 Hydrogen bonds: M:T.92, M:T.92 Salt bridges: M:R.102 ACY.31: 7 residues within 4Å: Chain D: F.82, V.114, R.117 Chain N: I.89, T.92, V.94, R.102 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain D Hydrophobic interactions: N:I.89, D:V.114 Hydrogen bonds: N:T.92, N:T.92 Salt bridges: N:R.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mura, C. et al., Structure and assembly of an augmented Sm-like archaeal protein 14-mer. Proc.Natl.Acad.Sci.USA (2003)

Release Date

2003-03-18

Peptides

small nuclear ribonucleoprotein homolog: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

E
S

F
T

G
U

H
V

I
W

J
X

K
Y

L
Z

M
1

N
2

small nuclear ribonucleoprotein homolog

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