SMTL ID : 2dgk.1 (5 other biounits)

Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: P.99, K.100, D.277, E.278 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.100, A:E.278 Water bridges: A:N.101, A:N.101, A:N.101, A:E.279 Salt bridges: A:K.100 SO4.4: 3 residues within 4Å: Chain B: K.100, D.277, E.278 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.100, B:E.278 Water bridges: B:N.101, B:E.279 SO4.8: 4 residues within 4Å: Chain C: P.99, K.100, D.277, E.278 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.100, C:E.278 Water bridges: C:N.101, C:E.279 Salt bridges: C:K.100 SO4.12: 4 residues within 4Å: Chain D: P.99, K.100, D.277, E.278 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.100, D:E.278 Water bridges: D:N.101, D:E.279 SO4.15: 3 residues within 4Å: Chain E: K.100, D.277, E.278 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.100, E:E.278 Salt bridges: E:K.100 SO4.18: 4 residues within 4Å: Chain F: P.99, K.100, D.277, E.278 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.100, F:E.278

6 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.2: 16 residues within 4Å: Chain A: G.111, S.112, S.113, Q.149, C.151, T.194, G.196, T.198, D.229, A.231, S.259, H.261, K.262, H.451 Chain B: F.303, S.304 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.149, A:Q.149, A:T.194, A:A.231, A:K.262 Hydrogen bonds: A:S.112, A:S.113, A:T.198, A:S.259, B:S.304 Water bridges: A:D.229, B:F.303 Salt bridges: A:H.261, A:K.262, A:H.451 PLP.5: 16 residues within 4Å: Chain A: F.303, S.304 Chain B: G.111, S.112, S.113, Q.149, C.151, T.194, G.196, T.198, D.229, A.231, S.259, H.261, K.262, H.451 16 PLIP interactions: 2 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:F.303, A:S.304, B:S.112, B:S.113, B:T.198, B:S.259 Hydrophobic interactions: B:Q.149, B:Q.149, B:T.194, B:A.231, B:K.262 Water bridges: B:E.114, B:Q.149 Salt bridges: B:H.261, B:K.262, B:H.451 PLP.9: 16 residues within 4Å: Chain C: G.111, S.112, S.113, Q.149, C.151, T.194, G.196, T.198, D.229, A.231, S.259, H.261, K.262, H.451 Chain D: F.303, S.304 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Q.149, C:Q.149, C:T.194, C:K.262 Hydrogen bonds: C:S.112, C:S.113, C:T.198, C:S.259, D:F.303, D:S.304 Water bridges: C:Q.149 Salt bridges: C:H.261, C:K.262, C:H.451 PLP.13: 16 residues within 4Å: Chain C: F.303, S.304 Chain D: G.111, S.112, S.113, Q.149, C.151, T.194, G.196, T.198, D.229, A.231, S.259, H.261, K.262, H.451 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.149, D:Q.149, D:T.194, D:K.262 Hydrogen bonds: D:S.112, D:S.113, D:T.198, D:S.259, C:F.303, C:S.304 Water bridges: D:Q.149, D:S.232 Salt bridges: D:H.261, D:K.262, D:H.451 PLP.16: 16 residues within 4Å: Chain E: G.111, S.112, S.113, Q.149, C.151, T.194, G.196, T.198, D.229, A.231, S.259, H.261, K.262, H.451 Chain F: F.303, S.304 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:Q.149, E:Q.149, E:T.194, E:K.262 Hydrogen bonds: E:S.112, E:S.113, E:T.198, E:S.259, F:S.304 Water bridges: E:Q.149, E:S.232, F:F.303 Salt bridges: E:H.261, E:K.262, E:H.451 PLP.19: 16 residues within 4Å: Chain E: F.303, S.304 Chain F: G.111, S.112, S.113, Q.149, C.151, T.194, G.196, T.198, D.229, A.231, S.259, H.261, K.262, H.451 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Q.149, F:T.194, F:K.262 Hydrogen bonds: F:S.112, F:S.113, F:S.113, F:T.198, F:S.259, F:S.259, E:F.303, E:S.304 Water bridges: F:Q.149, F:S.232 Salt bridges: F:H.261, F:K.262, F:H.451

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

EDO.3: 6 residues within 4Å: Chain A: Q.78, R.85 Chain B: E.35, L.38 Chain C: D.418, L.422 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:D.418, A:Q.78, A:R.85, A:R.85, B:E.35 EDO.6: 5 residues within 4Å: Chain A: N.67 Chain B: N.41, R.43, D.54 Chain C: Y.37 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.43, B:R.43 Water bridges: B:G.40, B:N.41, A:N.67 EDO.7: 5 residues within 4Å: Chain A: E.35 Chain B: Q.78, R.85 Chain F: D.418, L.422 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: B:Q.78, B:R.85, B:R.85, F:D.418, A:E.35 EDO.10: 4 residues within 4Å: Chain B: Y.37 Chain C: N.41, R.43, D.54 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.43, C:R.43 EDO.11: 7 residues within 4Å: Chain C: Q.78, R.85 Chain D: E.35, L.38 Chain E: D.418, F.419, L.422 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: C:Q.78, C:R.85, C:R.85, D:E.35, E:D.418 EDO.14: 6 residues within 4Å: Chain B: D.418, L.422 Chain C: E.35, L.38 Chain D: Q.78, R.85 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.78, D:R.85, D:R.85, C:E.35 EDO.17: 7 residues within 4Å: Chain A: D.418, F.419, L.422 Chain E: Q.78, R.85 Chain F: E.35, L.38 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.78, E:R.85, E:R.85, F:E.35 Water bridges: F:E.35 EDO.20: 7 residues within 4Å: Chain D: D.418, F.419, L.422 Chain E: E.35, L.38 Chain F: Q.78, R.85 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:Q.78, F:R.85, F:R.85, E:E.35 Water bridges: E:E.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gut, H. et al., Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB. Embo J. (2006)

Release Date

2006-06-20

Peptides

Glutamate decarboxylase beta: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate decarboxylase beta

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