SMTL ID : 5dcb.1

Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with PEP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: C.63, R.94, H.270, E.304, D.324 Ligands: PEP.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.63, A:H.270, A:E.304, A:D.324, H2O.1 MN.10: 5 residues within 4Å: Chain B: C.63, R.94, H.270, E.304, D.324 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.63, B:H.270, B:E.304, B:D.324, H2O.10 MN.15: 6 residues within 4Å: Chain C: C.63, R.94, K.99, H.270, E.304, D.324 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.63, C:H.270, C:E.304, C:D.324, H2O.16 MN.18: 5 residues within 4Å: Chain D: C.63, R.94, H.270, E.304, D.324 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.63, D:H.270, D:E.304, D:D.324, H2O.24

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

SO4.2: 3 residues within 4Å: Chain A: S.206, H.207, G.226 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.206, A:S.208, A:G.226 Salt bridges: A:H.207

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

EDO.3: 3 residues within 4Å: Chain A: R.256, A.257, G.259 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.257, A:A.258 EDO.4: 4 residues within 4Å: Chain A: G.193, N.194, L.195, K.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.195, A:K.196 Water bridges: A:G.193 EDO.11: 5 residues within 4Å: Chain B: W.106, D.112, L.115, D.116, G.117 No protein-ligand interaction detected (PLIP) EDO.19: 2 residues within 4Å: Chain D: A.337, L.338 1 PLIP interactions: 1 interactions with chain D Water bridges: D:L.338

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: W.106, D.112, L.115, D.116, G.117, D.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.313 Water bridges: A:G.105, A:W.106 PEG.20: 5 residues within 4Å: Chain D: W.106, D.112, L.115, G.117, D.313 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.313

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

PGE.6: 12 residues within 4Å: Chain A: Q.172, R.175, E.176, A.204, H.207, S.208, H.209 Chain B: R.101, T.102, T.103, V.104, K.107 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:G.105, B:K.107 Hydrogen bonds: A:Q.172, A:S.208

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.7: 9 residues within 4Å: Chain A: R.94, Y.96, K.99, E.145, K.188, R.236, H.270, M.302 Ligands: MN.1 10 PLIP interactions: 10 interactions with chain A Water bridges: A:R.94, A:K.99, A:E.145, A:K.188 Salt bridges: A:R.94, A:K.188, A:K.188, A:R.236, A:H.270, A:H.270 PEP.12: 8 residues within 4Å: Chain B: R.94, Y.96, K.99, E.145, K.188, R.236, H.270, M.302 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.96, B:D.267 Water bridges: B:R.94, B:K.99, B:E.145, B:E.145, B:R.236 Salt bridges: B:R.94, B:K.188, B:K.188, B:R.236, B:H.270, B:H.270 PEP.16: 8 residues within 4Å: Chain C: R.94, Y.96, K.99, E.145, K.188, R.236, H.270, M.302 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.145 Water bridges: C:R.94, C:R.94, C:E.145 Salt bridges: C:R.94, C:K.188, C:K.188, C:R.236, C:H.270, C:H.270 PEP.21: 8 residues within 4Å: Chain D: R.94, Y.96, K.99, E.145, K.188, R.236, H.270, M.302 9 PLIP interactions: 9 interactions with chain D Water bridges: D:R.94, D:K.99 Salt bridges: D:R.94, D:K.99, D:K.188, D:K.188, D:R.236, D:H.270, D:H.270

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.8: 14 residues within 4Å: Chain A: M.149, P.152, Q.153, A.156, L.177, G.180, L.181, S.182, F.211, S.213, K.216, V.223 Chain B: D.8, D.9 12 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:D.8, B:D.9, A:Q.153, A:S.182, A:K.216, F.8 Hydrophobic interactions: A:P.152, A:Q.153, A:L.177, A:F.211, A:V.223 Water bridges: A:D.157 PHE.13: 15 residues within 4Å: Chain A: D.8, D.9, I.12 Chain B: M.149, P.152, Q.153, A.156, L.177, G.180, L.181, S.182, F.211, S.213, K.216, V.223 13 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:P.152, B:Q.153, B:L.177, B:F.211, B:V.223, A:I.12 Hydrogen bonds: B:Q.153, B:S.182, B:K.216, A:D.8, A:D.9, F.13 Water bridges: B:D.157 PHE.17: 14 residues within 4Å: Chain C: M.149, P.152, Q.153, A.156, L.177, G.180, L.181, S.182, F.211, S.213, K.216, V.223 Chain D: D.8, D.9 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D, Hydrophobic interactions: C:P.152, C:Q.153, C:L.177, C:F.211, C:V.223 Hydrogen bonds: C:Q.153, C:S.182, C:K.216, D:D.8, D:D.9, D:D.9 Water bridges: C:D.157 PHE.22: 15 residues within 4Å: Chain C: T.7, D.8, D.9 Chain D: M.149, P.152, Q.153, A.156, L.177, G.180, L.181, S.182, F.211, S.213, K.216, V.223 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C, Hydrophobic interactions: D:P.152, D:Q.153, D:L.177, D:F.211, D:V.223 Hydrogen bonds: D:Q.153, D:S.182, D:K.216, C:D.8, C:D.9, C:D.9 Water bridges: D:D.157

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

CL.9: 2 residues within 4Å: Chain A: T.215, K.216 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: T.215, K.216 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: H.219 Chain D: H.219 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heyes, L.C. et al., Structure of Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with PEP at 2.05 Angstroms. To Be Published

Release Date

2016-08-24

Peptides

Phospho-2-dehydro-3-deoxyheptonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Phospho-2-dehydro-3-deoxyheptonate aldolase

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