SMTL ID : 3i3o.1 (1 other biounit)

2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: G.23, D.56, S.57, E.81 Ligands: NAE.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:S.57, A:E.81, H2O.6, H2O.6 MG.4: 5 residues within 4Å: Chain B: G.23, D.56, S.57, E.81 Ligands: NAE.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.56, B:S.57, B:E.81, H2O.10, H2O.11 MG.8: 5 residues within 4Å: Chain C: G.23, D.56, S.57, E.81 Ligands: NAE.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.56, C:S.57, C:E.81, H2O.17, H2O.18 MG.11: 5 residues within 4Å: Chain D: G.23, D.56, S.57, E.81 Ligands: NAE.13 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.56, D:S.57, D:E.81, H2O.26, H2O.28

4 x NAE: NICOTINAMIDE ADENINE DINUCLEOTIDE ACETONE ADDUCT(Non-covalent)

NAE.2: 35 residues within 4Å: Chain A: P.22, G.54, D.56, S.57, G.58, I.59, Y.78, L.79, E.81, G.104, D.105, L.106, N.132, V.133, A.134, Q.135, Q.136, I.156, Y.161, T.181, A.182, S.183, V.185, Y.196, K.200, P.226, G.227, P.228, I.229, T.231, P.232, L.233, I.234, F.246 Ligands: MG.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:P.226, A:L.233 Hydrogen bonds: A:S.57, A:S.57, A:S.57, A:I.59, A:L.79, A:E.81, A:D.105, A:D.105, A:L.106, A:N.132, A:A.134, A:Q.135, A:S.183, A:Y.196, A:K.200, A:I.229, A:I.229, A:T.231, A:T.231, A:L.233 Water bridges: A:G.60, A:E.81, A:N.132 NAE.5: 35 residues within 4Å: Chain B: P.22, G.54, D.56, S.57, G.58, I.59, Y.78, L.79, E.81, G.104, D.105, L.106, N.132, V.133, A.134, Q.135, Q.136, I.156, Y.161, T.181, A.182, S.183, V.185, Y.196, K.200, P.226, G.227, P.228, I.229, T.231, P.232, L.233, I.234, F.246 Ligands: MG.4 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.196, B:P.226, B:L.233 Hydrogen bonds: B:S.57, B:S.57, B:S.57, B:I.59, B:L.79, B:E.81, B:D.105, B:D.105, B:L.106, B:N.132, B:N.132, B:A.134, B:S.183, B:Y.196, B:K.200, B:I.229, B:I.229, B:T.231, B:L.233 Water bridges: B:G.60 NAE.9: 36 residues within 4Å: Chain C: P.22, G.54, D.56, S.57, G.58, I.59, G.60, Y.78, L.79, E.81, G.104, D.105, L.106, N.132, V.133, A.134, Q.135, Q.136, I.156, Y.161, T.181, A.182, S.183, V.185, Y.196, K.200, P.226, G.227, P.228, I.229, T.231, P.232, L.233, I.234, F.246 Ligands: MG.8 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:P.226, C:L.233 Hydrogen bonds: C:D.56, C:S.57, C:S.57, C:S.57, C:I.59, C:G.60, C:L.79, C:D.105, C:L.106, C:N.132, C:N.132, C:A.134, C:S.183, C:Y.196, C:K.200, C:I.229, C:I.229, C:T.231, C:L.233 NAE.13: 35 residues within 4Å: Chain D: P.22, G.54, D.56, S.57, G.58, I.59, Y.78, L.79, E.81, G.104, D.105, L.106, N.132, V.133, A.134, Q.135, Q.136, I.156, Y.161, T.181, A.182, S.183, V.185, Y.196, K.200, P.226, G.227, P.228, I.229, T.231, P.232, L.233, I.234, F.246 Ligands: MG.11 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:Y.196, D:P.226, D:L.233 Hydrogen bonds: D:S.57, D:S.57, D:S.57, D:I.59, D:L.79, D:E.81, D:D.105, D:D.105, D:L.106, D:N.132, D:N.132, D:A.134, D:Q.135, D:Y.161, D:S.183, D:Y.196, D:K.200, D:I.229, D:I.229, D:T.231, D:L.233 Water bridges: D:G.60, D:S.107

5 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 4 residues within 4Å: Chain A: E.109, K.113, K.166 Chain D: T.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.113, A:K.166, A:K.166 CAC.6: 3 residues within 4Å: Chain B: S.125, N.127, K.173 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.125, B:N.127, B:K.173, B:K.173 CAC.7: 4 residues within 4Å: Chain A: S.274 Chain B: R.254, Y.259, E.260 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.274, B:Y.259 Water bridges: B:R.254 CAC.10: 4 residues within 4Å: Chain B: T.146 Chain C: E.109, K.113, K.166 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.113, C:K.166, C:K.166 Water bridges: B:A.147 CAC.14: 5 residues within 4Å: Chain A: I.145, T.146 Chain D: E.109, K.113, K.166 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.113, D:K.166 Water bridges: D:E.109, A:A.147

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 2 residues within 4Å: Chain D: R.220, S.271 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halavaty, A.S. et al., 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone. To be Published

Release Date

2009-08-04

Peptides

Short chain dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Short chain dehydrogenase

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