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

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

Coordinates

PDB Format

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: H.28 Chain B: E.73 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.28, B:E.73, H2O.1, H2O.2, H2O.3 CD.2: 2 residues within 4Å: Chain A: E.73 Chain G: H.28 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: A:E.73, A:E.73, G:H.28, H2O.14, H2O.16 CD.5: 3 residues within 4Å: Chain B: H.28 Chain C: E.4, 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.3, H2O.8 CD.7: 3 residues within 4Å: Chain C: H.28, R.51 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.7 CD.8: 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.11 CD.9: 2 residues within 4Å: Chain E: H.28 Chain F: E.73 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: F:E.73, F:E.73, E:H.28, H2O.10, 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.13: 3 residues within 4Å: Chain H: H.28 Chain I: E.4 Ligands: GOL.15 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.28, H2O.19, H2O.22 CD.14: 2 residues within 4Å: Chain H: E.4 Chain N: H.28 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: H:E.4, N:H.28, H2O.32 CD.18: 2 residues within 4Å: Chain I: H.28 Chain J: E.4 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: J:E.4, I:H.28, H2O.21 CD.21: 1 residues within 4Å: Chain J: H.28 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:H.28, H2O.22, H2O.24 CD.23: 3 residues within 4Å: Chain D: K.80 Chain K: H.28 Chain L: E.4 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: L:E.4, K:H.28, H2O.24, H2O.26 CD.25: 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.25, H2O.26, H2O.27 CD.26: 1 residues within 4Å: Chain M: H.28 4 PLIP interactions: 1 interactions with chain M, 3 Ligand-Water interactions Metal complexes: M:H.28, H2O.28, H2O.28, H2O.31

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

NA.3: 3 residues within 4Å: Chain A: Q.14, V.16 Chain G: E.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.14 NA.6: 2 residues within 4Å: Chain B: E.47 Chain C: K.44 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.47, C:K.44

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: E.21, E.47, F.49 Chain B: Q.14, V.16, V.22 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.21, B:Q.14 GOL.12: 8 residues within 4Å: Chain G: A.75, K.76, E.79, V.86 Chain H: G.10, V.26, H.28, A.39 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:E.79 Water bridges: G:G.84, G:V.86 GOL.15: 6 residues within 4Å: Chain G: E.79 Chain H: H.28, N.50, R.51 Chain I: R.68 Ligands: CD.13 6 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G, 1 interactions with chain I Hydrogen bonds: H:N.50, H:N.50, I:R.68 Water bridges: H:N.50, H:R.51, G:K.80 GOL.16: 8 residues within 4Å: Chain H: E.21, Y.23, E.47, F.49 Chain I: Q.14, V.16, V.22, K.44 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Q.14, I:K.44 GOL.22: 7 residues within 4Å: Chain J: E.21, Y.23, E.47, F.49 Chain K: Q.14, V.22, K.44 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:Q.14, K:K.44, J:E.47 GOL.27: 7 residues within 4Å: Chain M: E.21, Y.23, E.47, F.49 Chain N: Q.14, V.16, V.22 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain N Hydrogen bonds: M:E.47, N:Q.14 Water bridges: M:N.19

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

ACY.11: 6 residues within 4Å: Chain F: E.21, E.47 Chain G: Q.14, V.16, V.22, K.44 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:K.44 ACY.17: 8 residues within 4Å: Chain A: F.82, P.113, V.114, R.117 Chain H: I.89, T.92, V.94, R.102 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain A Hydrophobic interactions: H:I.89, H:V.94, A:V.114 Salt bridges: H:R.102 Hydrogen bonds: A:P.113 ACY.19: 5 residues within 4Å: Chain I: R.11, E.12, S.64, T.65, E.66 7 PLIP interactions: 1 interactions with chain H, 6 interactions with chain I Water bridges: H:R.51 Hydrophobic interactions: I:R.11, I:E.66 Hydrogen bonds: I:T.65, I:E.66, I:E.66, I:E.66 ACY.20: 8 residues within 4Å: Chain G: 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 I, 3 interactions with chain G Hydrophobic interactions: I:I.89, G:P.113, G:V.114 Salt bridges: I:R.102 Hydrogen bonds: G:P.113 ACY.24: 8 residues within 4Å: Chain E: F.82, P.113, V.114, R.117 Chain K: I.89, T.92, V.94, R.102 6 PLIP interactions: 3 interactions with chain K, 3 interactions with chain E Hydrophobic interactions: K:I.89, E:P.113, E:V.114 Hydrogen bonds: K:T.92 Salt bridges: K:R.102 Water bridges: E:P.113 ACY.28: 8 residues within 4Å: Chain C: F.82, P.113, V.114, R.117 Chain M: I.89, T.92, V.94, R.102 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain M Hydrophobic interactions: C:P.113, C:V.114, M:I.89, M:V.94 Water bridges: C:R.120 Hydrogen bonds: M:T.92 Salt bridges: M:R.102 ACY.29: 7 residues within 4Å: Chain B: F.82, V.114, R.117 Chain N: I.89, T.92, V.94, R.102 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain N Hydrophobic interactions: B:V.114, N:I.89 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
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

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