SMTL ID : 1vm6.1

Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-tetramer

Ligands

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: H.139, H.140, K.143 Ligands: ACT.2, NAD.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.196 Salt bridges: A:H.140, A:K.143 ACT.2: 9 residues within 4Å: Chain A: T.85, Y.108, K.143, D.145, S.148, G.149, T.150 Ligands: ACT.1, NAD.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.85 Hydrogen bonds: A:G.149, A:T.150, A:T.150, A:T.150 Water bridges: A:N.109 Salt bridges: A:H.139, A:K.143 ACT.4: 6 residues within 4Å: Chain A: I.194, S.195 Chain B: G.171, P.173, S.195, R.196 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.173, A:I.194 Hydrogen bonds: B:R.196 Water bridges: B:R.196 Salt bridges: B:R.196 ACT.5: 6 residues within 4Å: Chain B: H.139, H.140, K.143, P.173 Ligands: ACT.9, NAD.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.173 Water bridges: B:R.196, B:R.196 Salt bridges: B:H.139, B:H.140, B:K.143 ACT.6: 5 residues within 4Å: Chain B: V.177, E.188 Chain D: V.136, T.138, L.167 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.136 Hydrogen bonds: D:T.138 Water bridges: D:D.175 ACT.7: 5 residues within 4Å: Chain B: S.122, V.125, K.126, A.157, G.159 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.126 ACT.8: 7 residues within 4Å: Chain B: F.110, I.112, V.198, I.201, G.202, K.205, F.220 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.112, B:K.205, B:F.220 Hydrogen bonds: B:G.202 Water bridges: B:K.205, B:K.205, C:E.185, C:E.185 Salt bridges: B:K.205 ACT.9: 9 residues within 4Å: Chain B: T.85, Y.108, K.143, D.145, S.148, G.149, T.150 Ligands: ACT.5, NAD.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.85 Hydrogen bonds: B:T.85, B:T.85, B:G.149, B:T.150 Water bridges: B:N.109 Salt bridges: B:H.139, B:K.143 ACT.14: 7 residues within 4Å: Chain C: D.55, G.79, P.103, L.210, V.211, G.212, K.213 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.103 Hydrogen bonds: C:D.55, C:G.212, C:K.213 ACT.15: 5 residues within 4Å: Chain B: F.120, L.124 Chain C: F.120, E.123, F.225 No protein-ligand interaction detected (PLIP) ACT.19: 6 residues within 4Å: Chain D: P.63, T.84, T.85, K.144, D.145 Ligands: NAD.21 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.144 Hydrogen bonds: D:T.85, D:D.145 Water bridges: D:D.145, D:D.145 Salt bridges: D:K.143 ACT.20: 8 residues within 4Å: Chain D: T.85, Y.108, K.143, D.145, S.148, G.149, T.150 Ligands: NAD.21 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.85, D:G.149, D:T.150, D:T.150 Water bridges: D:T.150 Salt bridges: D:H.139, D:K.143

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

NAD.3: 25 residues within 4Å: Chain A: G.19, Y.20, S.21, G.22, R.23, M.24, D.44, V.45, F.60, S.61, S.62, E.64, A.65, G.83, T.84, T.85, A.107, Y.108, N.109, F.110, K.143, D.145, F.199 Ligands: ACT.1, ACT.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.19, A:S.21, A:G.22, A:R.23, A:M.24, A:D.44, A:V.45, A:S.61, A:S.62, A:G.83, A:T.85, A:F.110, A:K.143, A:D.145 Water bridges: A:R.23, A:R.23, A:R.23, A:G.25, A:T.85 Salt bridges: A:R.23, A:R.23, A:K.144 pi-Stacking: A:F.60, A:F.199 NAD.10: 25 residues within 4Å: Chain B: G.19, Y.20, S.21, G.22, R.23, M.24, D.44, V.45, F.60, S.61, S.62, E.64, A.65, G.83, T.84, T.85, A.107, Y.108, N.109, F.110, K.143, D.145, F.199 Ligands: ACT.5, ACT.9 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.19, B:S.21, B:G.22, B:R.23, B:M.24, B:V.45, B:S.61, B:S.62, B:E.64, B:G.83, B:T.85, B:F.110, B:D.145 Water bridges: B:S.21, B:S.21, B:R.23, B:R.23, B:G.25, B:K.144, B:D.145 Salt bridges: B:R.23, B:R.23 pi-Stacking: B:F.60, B:F.199 NAD.16: 21 residues within 4Å: Chain C: G.19, S.21, G.22, R.23, M.24, D.44, V.45, F.60, S.61, S.62, E.64, A.65, G.83, T.84, T.85, A.107, Y.108, N.109, F.110, F.199 Ligands: PG4.18 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.60 Hydrogen bonds: C:G.19, C:S.21, C:S.21, C:G.22, C:R.23, C:M.24, C:V.45, C:S.61, C:S.62, C:E.64, C:G.83, C:T.85, C:F.110 Salt bridges: C:R.23, C:R.23 pi-Stacking: C:F.199 NAD.21: 25 residues within 4Å: Chain D: G.19, Y.20, S.21, G.22, R.23, M.24, D.44, V.45, F.60, S.61, S.62, A.65, G.83, T.84, T.85, A.107, Y.108, N.109, F.110, K.143, K.144, D.145, F.199 Ligands: ACT.19, ACT.20 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:F.60, D:F.199 Hydrogen bonds: D:G.19, D:S.21, D:S.21, D:G.22, D:R.23, D:M.24, D:V.45, D:S.61, D:S.62, D:G.83, D:T.85, D:F.110, D:D.145 Water bridges: D:G.25, D:S.62, D:K.143, D:K.144, D:K.144, D:K.144 Salt bridges: D:R.23, D:R.23, D:K.144 pi-Stacking: D:F.199

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 6 residues within 4Å: Chain B: Y.20, Q.29, L.39, K.42, E.49, L.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.42, B:E.49 PG4.12: 7 residues within 4Å: Chain B: L.87, K.88, L.92, Q.106, Y.108, L.153, S.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.106 PG4.13: 3 residues within 4Å: Chain B: R.119, F.120, F.225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.119 PG4.18: 7 residues within 4Å: Chain C: Y.108, N.109, P.173, S.195, R.196, F.199 Ligands: NAD.16 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.109, C:R.196

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

EDO.17: 4 residues within 4Å: Chain C: R.96, S.99, G.216, M.217 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.99, C:M.217

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution. To be published

Release Date

2004-09-21

Peptides

Dihydrodipicolinate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dihydrodipicolinate reductase