SMTL ID : 4uc5.1

Neisseria Meningitidis DAH7PS-Phenylalanine regulated

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: C.63, R.94, H.270, E.304, D.324 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.2 MN.6: 5 residues within 4Å: Chain B: C.63, R.94, H.270, E.304, D.324 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:H.270, B:E.304, B:D.324 MN.9: 4 residues within 4Å: Chain C: C.63, H.270, E.304, D.324 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.63, C:H.270, C:E.304, C:D.324 MN.11: 4 residues within 4Å: Chain D: C.63, H.270, E.304, D.324 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.63, D:H.270, D:E.304, D:D.324

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

PEG.2: 4 residues within 4Å: Chain A: W.106, L.115, G.117, D.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.313

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

SO4.3: 7 residues within 4Å: Chain A: A.217, G.218, H.219 Chain B: H.219 Chain C: H.219 Chain D: A.217, H.219 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Salt bridges: A:H.219, B:H.219, D:H.219, C:H.219 SO4.4: 5 residues within 4Å: Chain A: G.165, A.166, K.188, R.236, H.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.166 Water bridges: A:R.236 Salt bridges: A:K.188, A:R.236, A:H.270 SO4.7: 5 residues within 4Å: Chain B: G.165, A.166, K.188, R.236, H.270 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.166 Water bridges: B:R.167 Salt bridges: B:K.188, B:R.236, B:H.270 SO4.12: 5 residues within 4Å: Chain D: G.165, A.166, K.188, R.236, H.270 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.166 Water bridges: D:R.167 Salt bridges: D:K.188, D:R.236, D:H.270

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.5: 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 11 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions, 2 interactions with chain B Hydrophobic interactions: A:P.152, A:Q.153, A:L.177, A:F.211, A:V.223 Hydrogen bonds: A:Q.153, A:S.182, A:K.216, F.5, B:D.8, B:D.9 PHE.8: 13 residues within 4Å: Chain A: D.8, D.9 Chain B: M.149, P.152, Q.153, A.156, G.180, L.181, S.182, F.211, S.213, K.216, V.223 11 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:P.152, B:Q.153, B:F.211, B:F.211, B:V.223 Hydrogen bonds: B:Q.153, B:S.182, B:K.216, A:D.8, A:D.9, F.8 PHE.10: 13 residues within 4Å: Chain C: M.149, P.152, Q.153, A.156, G.180, L.181, S.182, F.211, S.213, K.216, V.223 Chain D: D.8, D.9 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:P.152, C:Q.153, 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 PHE.13: 14 residues within 4Å: Chain C: 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 14 PLIP interactions: 4 interactions with chain C, 9 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: C:D.8, C:D.8, C:D.9, C:D.9, D:Q.153, D:S.182, D:K.216, F.13 Hydrophobic interactions: D:P.152, D:Q.153, D:L.177, D:F.211, D:V.223 Water bridges: D:D.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lang, E.J. et al., Calculated Pka Variations Expose Dynamic Allosteric Communication Networks. J.Am.Chem.Soc. (2016)

Release Date

2015-11-25

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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