SMTL ID : 6c5c.1

Crystal structure of the 3-dehydroquinate synthase (DHQS) domain of Aro1 from Candida albicans SC5314 in complex with NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: D.45, N.47, M.48, P.81, E.83, K.86, G.114, G.115, V.116, D.119, T.139, T.140, L.142, D.146, S.147, K.152, N.162, F.179, T.182, L.183, P.184, Q.187 Ligands: EDO.9 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.45, A:N.47, A:E.83, A:G.115, A:V.116, A:D.119, A:T.139, A:T.140, A:N.162, A:F.179, A:T.182 Water bridges: A:D.45, A:K.86, A:K.86, A:G.114, A:G.114, A:D.119, A:K.152, A:Q.187, A:N.190, A:N.190, A:K.246 NAD.12: 22 residues within 4Å: Chain B: D.45, N.47, M.48, P.81, E.83, K.86, G.114, G.115, V.116, D.119, T.139, T.140, L.142, D.146, S.147, K.152, N.162, F.179, T.182, L.183, Q.187 Ligands: EDO.15 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.45, B:N.47, B:E.83, B:G.115, B:V.116, B:D.119, B:D.119, B:T.140, B:T.140, B:N.162, B:F.179 Water bridges: B:D.45, B:K.152, B:T.182, B:Q.187, B:N.190, B:N.190

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: T.46, C.78, V.79 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.46 Water bridges: A:T.46, A:C.78, A:C.78, A:C.78 EDO.3: 5 residues within 4Å: Chain A: A.49, Y.54, T.76, Y.77, C.78 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.54, A:T.76, A:Y.77 Water bridges: A:T.44, A:T.58, A:T.58, A:T.76 EDO.4: 2 residues within 4Å: Chain A: F.97, Q.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.101 EDO.5: 8 residues within 4Å: Chain A: I.11, V.149, G.150, G.151, Q.169, P.170, V.173, V.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.150, A:G.150 Water bridges: A:Q.169 EDO.6: 2 residues within 4Å: Chain A: R.88, P.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.88 Water bridges: A:R.88 EDO.7: 5 residues within 4Å: Chain A: V.307, A.308, R.311, K.368, I.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.311, A:R.311, A:I.369 EDO.8: 3 residues within 4Å: Chain A: P.306, V.307, A.310 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: D.146, K.197, K.246, L.263 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.263 Water bridges: A:K.197 EDO.10: 4 residues within 4Å: Chain A: E.211, S.214, K.314, C.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.214 Water bridges: A:C.315 EDO.13: 6 residues within 4Å: Chain A: F.163 Chain B: L.99, G.102, C.103, T.104, M.129 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.99 EDO.14: 7 residues within 4Å: Chain B: I.11, V.149, G.150, G.151, Q.169, P.170, V.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.150, B:G.150 Water bridges: B:Q.169 EDO.15: 5 residues within 4Å: Chain B: D.146, K.197, L.263, H.267 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.263 Water bridges: B:K.197, B:K.246 EDO.16: 6 residues within 4Å: Chain B: I.273, I.289, K.293, S.324, I.325, L.389 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.293, B:I.325

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

CL.11: 4 residues within 4Å: Chain A: K.91, F.123 Chain B: K.91, F.123 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J. et al., Molecular analysis and essentiality of Aro1 shikimate biosynthesis multi-enzyme in Candida albicans. Life Sci Alliance (2022)

Release Date

2018-01-24

Peptides

3-dehydroquinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-dehydroquinate synthase