SMTL ID : 3ijr.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 33 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, I.156, Y.161, T.181, A.182, S.183, Y.196, K.200, P.226, G.227, P.228, I.229, T.231, P.232, L.233, I.234, F.246 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain A 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:Y.161, A:Y.196, A:K.200, A:I.229, A:I.229, A:T.231, A:L.233 Water bridges: A:E.81, A:S.107, A:N.132, A:N.132 NAD.4: 33 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, I.156, Y.161, T.181, A.182, S.183, Y.196, K.200, P.226, G.227, P.228, I.229, T.231, P.232, L.233, I.234, F.246 Ligands: MG.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:P.226 Hydrogen bonds: B:S.57, B:S.57, B:S.57, B:I.59, B:L.79, B:E.81, B:D.105, B:L.106, B:S.107, B:N.132, B:N.132, B:A.134, B:K.200, B:I.229, B:I.229, B:T.231, B:T.231, B:L.233 Water bridges: B:G.60, B:G.60 NAD.8: 34 residues within 4Å: Chain C: P.22, G.54, D.56, S.57, G.58, I.59, Y.78, L.79, E.81, G.104, D.105, L.106, S.107, N.132, V.133, A.134, Q.135, I.156, Y.161, T.181, A.182, S.183, Y.196, K.200, P.226, G.227, P.228, I.229, T.231, P.232, L.233, I.234, F.246 Ligands: MG.9 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.226 Hydrogen bonds: C:S.57, C:S.57, C:S.57, C:I.59, C:L.79, C:E.81, C:D.105, C:L.106, C:S.107, C:N.132, C:N.132, C:A.134, C:K.200, C:I.229, C:I.229, C:T.231, C:T.231, C:L.233 Water bridges: C:Q.136 NAD.12: 33 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, I.156, Y.161, T.181, A.182, S.183, Y.196, K.200, P.226, G.227, P.228, I.229, T.231, P.232, L.233, I.234, F.246 Ligands: MG.13 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:P.226 Hydrogen bonds: 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:Y.196, D:K.200, D:I.229, D:I.229, D:T.231, D:L.233 Water bridges: D:E.81

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.23, D.56, S.57, E.81 Ligands: NAD.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:S.57, A:E.81, H2O.2, H2O.3 MG.5: 5 residues within 4Å: Chain B: G.23, D.56, S.57, E.81 Ligands: NAD.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.56, B:S.57, B:E.81, H2O.6, H2O.6 MG.9: 5 residues within 4Å: Chain C: G.23, D.56, S.57, E.81 Ligands: NAD.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.56, C:S.57, C:E.81, H2O.8, H2O.8 MG.13: 5 residues within 4Å: Chain D: G.23, D.56, S.57, E.81 Ligands: NAD.12 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.56, D:S.57, D:E.81, H2O.12, H2O.12

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: E.109, K.113, K.166 Chain D: T.146 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Water bridges: A:K.166, A:K.166, D:A.147 Salt bridges: A:K.113, A:K.166 SO4.6: 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 Water bridges: B:S.125 Salt bridges: B:K.173 SO4.7: 4 residues within 4Å: Chain B: K.113, K.166 Chain C: I.145, T.146 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.166, B:K.166 Salt bridges: B:K.113, B:K.166 SO4.10: 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 Water bridges: C:K.166, B:A.147 Salt bridges: C:K.113, C:K.166 SO4.11: 7 residues within 4Å: Chain C: G.175, V.177, R.220, S.270, S.271, S.273, S.274 5 PLIP interactions: 5 interactions with chain C Water bridges: C:G.175, C:G.175, C:A.269, C:S.274 Salt bridges: C:R.220 SO4.14: 4 residues within 4Å: Chain A: T.146 Chain D: E.109, K.113, K.166 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain D Water bridges: A:A.147, D:K.113, D:K.113, D:K.166 Salt bridges: D:K.113, D:K.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halavaty, A.S. et al., 2.05 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD+. To be Published

Release Date

2009-09-08

Peptides

Oxidoreductase, short chain dehydrogenase/reductase family: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Oxidoreductase, short chain dehydrogenase/reductase family

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