SMTL ID : 5ees.1

Crystal structure of DapB in complex with NADP+ from Corynebacterium glutamicum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: D.139, A.140, P.141 Chain C: Q.170, L.172 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:A.140 Hydrogen bonds: C:Q.170 GOL.5: 5 residues within 4Å: Chain B: D.139, A.140, P.141 Chain D: Q.170, L.172 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Water bridges: B:A.140 Hydrogen bonds: D:Q.170 GOL.9: 5 residues within 4Å: Chain A: Q.170, L.172 Chain C: D.139, A.140, P.141 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.170 Water bridges: C:A.140 GOL.13: 5 residues within 4Å: Chain B: Q.170, L.172 Chain D: D.139, A.140, P.141 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.170 Water bridges: D:A.140

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 21 residues within 4Å: Chain A: G.8, K.10, G.11, R.12, V.13, I.33, G.34, V.35, F.53, T.54, T.55, A.58, N.62, G.76, T.77, T.78, A.103, P.104, N.105, F.106, F.220 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.13 Hydrogen bonds: A:G.8, A:K.10, A:R.12, A:V.13, A:T.54, A:N.62, A:N.62, A:T.78, A:F.106 Water bridges: A:G.11, A:G.14, A:V.35, A:T.78, A:P.104, A:N.105 Salt bridges: A:R.12 pi-Stacking: A:F.53, A:F.220 NAP.6: 21 residues within 4Å: Chain B: G.8, K.10, G.11, R.12, V.13, I.33, G.34, V.35, F.53, T.54, T.55, A.58, N.62, G.76, T.77, T.78, A.103, P.104, N.105, F.106, F.220 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.13 Hydrogen bonds: B:G.8, B:K.10, B:R.12, B:V.13, B:T.54, B:N.62, B:N.62, B:T.78, B:F.106 Water bridges: B:G.11, B:G.14, B:V.35, B:T.78, B:P.104, B:N.105 Salt bridges: B:R.12 pi-Stacking: B:F.53, B:F.220 NAP.10: 21 residues within 4Å: Chain C: G.8, K.10, G.11, R.12, V.13, I.33, G.34, V.35, F.53, T.54, T.55, A.58, N.62, G.76, T.77, T.78, A.103, P.104, N.105, F.106, F.220 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:V.13 Hydrogen bonds: C:G.8, C:K.10, C:R.12, C:V.13, C:T.54, C:N.62, C:N.62, C:T.78, C:F.106 Water bridges: C:G.11, C:G.14, C:V.35, C:T.78, C:P.104, C:N.105 Salt bridges: C:R.12 pi-Stacking: C:F.53, C:F.220 NAP.14: 21 residues within 4Å: Chain D: G.8, K.10, G.11, R.12, V.13, I.33, G.34, V.35, F.53, T.54, T.55, A.58, N.62, G.76, T.77, T.78, A.103, P.104, N.105, F.106, F.220 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:V.13 Hydrogen bonds: D:G.8, D:K.10, D:R.12, D:V.13, D:T.54, D:N.62, D:N.62, D:T.78, D:F.106 Water bridges: D:G.11, D:G.14, D:V.35, D:T.78, D:P.104, D:N.105 Salt bridges: D:R.12 pi-Stacking: D:F.53, D:F.220

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

SO4.3: 5 residues within 4Å: Chain A: K.137, D.139, S.142, G.143, T.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.143, A:T.144 Salt bridges: A:K.137 SO4.4: 2 residues within 4Å: Chain A: H.134, K.137 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.139 Salt bridges: A:H.134, A:K.137 SO4.7: 5 residues within 4Å: Chain B: K.137, D.139, S.142, G.143, T.144 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.143, B:T.144, B:T.144 Salt bridges: B:K.137 SO4.8: 2 residues within 4Å: Chain B: H.134, K.137 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.134, B:K.137 SO4.11: 5 residues within 4Å: Chain C: K.137, D.139, S.142, G.143, T.144 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.143, C:T.144 Salt bridges: C:K.137 SO4.12: 2 residues within 4Å: Chain C: H.134, K.137 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.139 Salt bridges: C:H.134, C:K.137 SO4.15: 5 residues within 4Å: Chain D: K.137, D.139, S.142, G.143, T.144 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.143, D:T.144, D:T.144 Salt bridges: D:K.137 SO4.16: 2 residues within 4Å: Chain D: H.134, K.137 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:H.134, D:K.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sagong, H.Y. et al., Structural Insight into Dihydrodipicolinate Reductase from Corybebacterium glutamicum for Lysine Biosynthesis. J. Microbiol. Biotechnol. (2016)

Release Date

2015-11-11

Peptides

4-hydroxy-tetrahydrodipicolinate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

4-hydroxy-tetrahydrodipicolinate reductase

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