SMTL ID : 1ud5.2 (1 other biounit)

Crystal structure of AmyK38 with rubidium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: N.104, D.194, N.200, H.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.104, A:D.194, A:N.200, A:H.235 NA.2: 6 residues within 4Å: Chain A: G.300, S.301, Y.302, W.403, D.404, N.427 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.302, A:N.427 NA.9: 4 residues within 4Å: Chain B: N.104, D.194, N.200, H.235 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.104, B:N.104, B:N.200 NA.10: 6 residues within 4Å: Chain B: G.300, S.301, Y.302, W.403, D.404, N.427 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.404, B:N.427, B:N.427 NA.17: 4 residues within 4Å: Chain C: N.104, D.194, N.200, H.235 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.104, C:D.194, C:N.200 NA.18: 6 residues within 4Å: Chain C: G.300, S.301, Y.302, W.403, D.404, N.427 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.302, C:D.404, C:N.427

18 x RB: RUBIDIUM ION(Non-covalent)

RB.3: 5 residues within 4Å: Chain A: N.289, V.324, D.325, S.337, V.339 Ligand excluded by PLIP RB.4: 4 residues within 4Å: Chain A: N.68, Q.69, S.144 Chain C: N.452 Ligand excluded by PLIP RB.5: 3 residues within 4Å: Chain A: R.249, N.250, A.252 Ligand excluded by PLIP RB.6: 3 residues within 4Å: Chain A: T.445, N.479, Q.480 Ligand excluded by PLIP RB.7: 3 residues within 4Å: Chain A: E.411, S.419, N.441 Ligand excluded by PLIP RB.8: 2 residues within 4Å: Chain A: E.383, T.450 Ligand excluded by PLIP RB.11: 5 residues within 4Å: Chain B: N.289, V.324, D.325, S.337, V.339 Ligand excluded by PLIP RB.12: 4 residues within 4Å: Chain A: N.452 Chain B: N.68, Q.69, S.144 Ligand excluded by PLIP RB.13: 3 residues within 4Å: Chain B: R.249, N.250, A.252 Ligand excluded by PLIP RB.14: 3 residues within 4Å: Chain B: T.445, N.479, Q.480 Ligand excluded by PLIP RB.15: 3 residues within 4Å: Chain B: E.411, S.419, N.441 Ligand excluded by PLIP RB.16: 2 residues within 4Å: Chain B: E.383, T.450 Ligand excluded by PLIP RB.19: 5 residues within 4Å: Chain C: N.289, V.324, D.325, S.337, V.339 Ligand excluded by PLIP RB.20: 4 residues within 4Å: Chain B: N.452 Chain C: N.68, Q.69, S.144 Ligand excluded by PLIP RB.21: 3 residues within 4Å: Chain C: R.249, N.250, A.252 Ligand excluded by PLIP RB.22: 3 residues within 4Å: Chain C: T.445, N.479, Q.480 Ligand excluded by PLIP RB.23: 3 residues within 4Å: Chain C: E.411, S.419, N.441 Ligand excluded by PLIP RB.24: 2 residues within 4Å: Chain C: E.383, T.450 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nonaka, T. et al., Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites. J.Biol.Chem. (2003)

Release Date

2003-07-22

Peptides

amylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

amylase

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