SMTL ID : 5ugv.1

DapB from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 13 residues within 4Å: Chain A: G.32, K.34, G.35, K.36, V.37, D.58, A.59, F.77, T.78, V.82, G.100, T.101, T.102 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.32, A:K.36, A:V.37, A:T.102 Water bridges: A:G.35, A:G.38 NAD.5: 20 residues within 4Å: Chain B: L.31, G.32, K.34, G.35, K.36, V.37, L.57, D.58, A.59, F.77, T.78, V.82, N.86, G.100, T.101, T.102, A.127, P.128, N.129, F.130 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.32, B:K.36, B:V.37, B:A.59, B:N.86, B:N.86, B:G.100, B:T.102, B:F.130 Water bridges: B:G.35, B:G.38 pi-Stacking: B:F.77 NAD.6: 13 residues within 4Å: Chain C: G.32, K.34, G.35, K.36, V.37, D.58, A.59, F.77, T.78, V.82, G.100, T.101, T.102 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.32, C:K.36, C:V.37, C:T.102 Water bridges: C:G.35, C:G.38 NAD.10: 20 residues within 4Å: Chain D: L.31, G.32, K.34, G.35, K.36, V.37, L.57, D.58, A.59, F.77, T.78, V.82, N.86, G.100, T.101, T.102, A.127, P.128, N.129, F.130 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.32, D:K.36, D:V.37, D:A.59, D:N.86, D:N.86, D:G.100, D:T.102, D:F.130 Water bridges: D:G.35, D:G.38 pi-Stacking: D:F.77

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

SO4.2: 5 residues within 4Å: Chain A: K.161, S.166, G.167, T.168, R.171 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.166, A:G.167, A:T.168, A:T.168, A:R.171, A:R.171 Salt bridges: A:K.161 SO4.7: 5 residues within 4Å: Chain C: K.161, S.166, G.167, T.168, R.171 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.166, C:G.167, C:T.168, C:T.168, C:R.171, C:R.171 Salt bridges: C:K.161

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 11 residues within 4Å: Chain A: E.220, L.222, T.229, T.231 Chain B: D.235, L.237 Chain D: L.215, H.218, E.220, R.233 Ligands: PGE.8 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.233, D:R.233 PGE.4: 13 residues within 4Å: Chain A: I.154, L.156, L.215, H.218, E.220, R.233 Chain C: D.235 Chain D: I.154, E.220, L.222, T.229, T.231 Ligands: PGE.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.233, A:R.233 PGE.8: 11 residues within 4Å: Chain B: L.215, H.218, E.220, R.233 Chain C: E.220, L.222, T.229, T.231 Chain D: D.235, L.237 Ligands: PGE.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.233, B:R.233 PGE.9: 13 residues within 4Å: Chain A: D.235 Chain B: I.154, E.220, L.222, T.229, T.231 Chain C: I.154, L.156, L.215, H.218, E.220, R.233 Ligands: PGE.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.233, C:R.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pote, S. et al., Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus. Biochim Biophys Acta Gen Subj (2021)

Release Date

2018-01-17

Peptides

4-hydroxy-tetrahydrodipicolinate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

4-hydroxy-tetrahydrodipicolinate reductase