SMTL ID : 3flu.1

Crystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: N.86, Y.112 Chain B: N.86, E.90, Y.112 Ligands: GOL.7, GOL.18 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: Y.139, R.144, G.192, V.211, F.250 Ligands: SO4.3 Ligand excluded by PLIP SO4.3: 10 residues within 4Å: Chain A: A.14, V.46, G.49, T.50, T.51, L.107, Y.139, K.167, I.209 Ligands: SO4.2 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: K.218, L.219, R.241, Q.296 Ligands: GOL.8 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: H.195, F.250 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: M.7, P.184, E.185, G.186, H.206 Ligand excluded by PLIP SO4.14: 9 residues within 4Å: Chain B: A.14, G.49, T.50, T.51, L.107, Y.139, K.167, I.209 Ligands: SO4.16 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: H.195, F.250 Ligand excluded by PLIP SO4.16: 8 residues within 4Å: Chain B: Y.139, V.141, R.144, K.167, A.169, G.192, F.250 Ligands: SO4.14 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: T.150, N.151, S.175 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain C: N.86, E.90, Y.112 Chain D: N.86, E.90, Y.112 Ligands: GOL.29, GOL.40 Ligand excluded by PLIP SO4.25: 10 residues within 4Å: Chain C: A.14, G.49, T.50, T.51, L.107, Y.139, K.167, I.209 Ligands: SO4.28, GOL.34 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: E.185, G.186, F.187, H.206 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: H.195, F.250 Ligand excluded by PLIP SO4.28: 7 residues within 4Å: Chain C: Y.139, V.141, R.144, K.167, G.192, F.250 Ligands: SO4.25 Ligand excluded by PLIP SO4.37: 8 residues within 4Å: Chain D: Y.139, V.141, R.144, A.169, G.192, F.250 Ligands: GOL.35, SO4.38 Ligand excluded by PLIP SO4.38: 10 residues within 4Å: Chain D: A.14, G.49, T.50, T.51, L.107, Y.139, K.167, I.209 Ligands: SO4.37, GOL.41 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain D: H.195, F.250 Ligands: GOL.35 Ligand excluded by PLIP

29 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: I.25, H.26, Y.27, E.28, R.31 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: S.54, A.55, G.84, Y.112 Chain B: N.86, Y.113 Ligands: SO4.1 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: W.36, N.40, A.216, P.217, K.218, Q.296 Ligands: SO4.4 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: W.260, S.263, A.264, P.270 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: N.20, Q.21, E.269, H.271 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: S.117, Q.118 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: T.150, N.151, D.152, S.175 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: W.260, S.263, A.264, P.270 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: N.86, Y.113 Chain B: S.54, A.55, G.84, Y.112 Ligands: SO4.1 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: R.236, E.237, D.240 Chain D: N.181 Ligand excluded by PLIP GOL.20: 2 residues within 4Å: Chain B: W.36, R.267 Ligand excluded by PLIP GOL.21: 2 residues within 4Å: Chain B: S.117, Q.118 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: T.150, N.151, D.152, S.175, R.182 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain C: S.54, A.55, G.84, Y.112 Chain D: N.86, Y.113 Ligands: SO4.24, GOL.34 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain C: W.260, S.263, A.264, Q.284 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain C: N.151, D.152, L.155, E.178, R.182 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain C: T.280, E.281, N.282 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain C: W.36, N.40, P.217, K.218 Ligand excluded by PLIP GOL.34: 13 residues within 4Å: Chain C: V.48, G.49, T.50, S.54, G.82, T.83, G.84, L.107, S.108, V.109 Chain D: Y.113 Ligands: SO4.25, GOL.29 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain C: K.115 Chain D: V.141, G.143, R.144, F.250 Ligands: SO4.37, SO4.39 Ligand excluded by PLIP GOL.36: 2 residues within 4Å: Chain C: S.117, Q.118 Ligand excluded by PLIP GOL.40: 8 residues within 4Å: Chain C: N.86, Y.113 Chain D: S.54, A.55, G.84, Y.112 Ligands: SO4.24, GOL.41 Ligand excluded by PLIP GOL.41: 14 residues within 4Å: Chain C: Y.113 Chain D: V.48, G.49, T.50, S.54, G.82, T.83, G.84, L.107, S.108, V.109, Y.139 Ligands: SO4.38, GOL.40 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain D: I.25, H.26, Y.27, E.28, R.31 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain B: H.195, D.247 Chain D: N.172, G.174, S.175, E.178 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain D: W.260, S.263, A.264, P.270 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain D: N.20, Q.21, E.269, H.271 Ligand excluded by PLIP GOL.46: 4 residues within 4Å: Chain D: T.150, N.151, D.152, S.175 Ligand excluded by PLIP GOL.47: 2 residues within 4Å: Chain D: S.117, Q.118 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devenish, S.R.A. et al., Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis. Biochim.Biophys.Acta (2009)

Release Date

2009-06-23

Peptides

Dihydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dihydrodipicolinate synthase