SMTL ID : 1htq.2 (1 other biounit)

Multicopy crystallographic structure of a relaxed glutamine synthetase from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.132, A:E.132, A:E.365 MN.4: 6 residues within 4Å: Chain B: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.132, B:E.132, B:E.365 MN.7: 6 residues within 4Å: Chain C: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.132, C:E.132, C:E.365 MN.10: 6 residues within 4Å: Chain D: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.132, D:E.132, D:E.365 MN.13: 6 residues within 4Å: Chain E: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.14 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.132, E:E.132, E:E.365 MN.16: 6 residues within 4Å: Chain F: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.17 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.132, F:E.132, F:E.365 MN.19: 6 residues within 4Å: Chain G: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.20 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.132, G:E.132, G:E.365 MN.22: 6 residues within 4Å: Chain H: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.23 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.132, H:E.132, H:E.365 MN.25: 6 residues within 4Å: Chain I: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.26 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.132, I:E.132, I:E.365 MN.28: 6 residues within 4Å: Chain J: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.29 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.132, J:E.132, J:E.365 MN.31: 6 residues within 4Å: Chain K: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.32 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.132, K:E.132, K:E.365 MN.34: 6 residues within 4Å: Chain L: E.132, H.275, R.351, E.365, R.367 Ligands: AMP.35 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.132, L:E.132, L:E.365

12 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 17 residues within 4Å: Chain A: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.132, A:N.228, A:F.231, A:S.279, A:W.281, A:R.351 Water bridges: A:Y.229, A:Y.229 Salt bridges: A:H.277 pi-Stacking: A:F.231, A:F.231 AMP.5: 17 residues within 4Å: Chain B: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:E.132, B:N.228, B:F.231, B:S.279, B:W.281, B:R.351 Water bridges: B:Y.229, B:Y.229 Salt bridges: B:H.277 pi-Stacking: B:F.231, B:F.231 AMP.8: 17 residues within 4Å: Chain C: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.132, C:N.228, C:F.231, C:S.279, C:W.281, C:R.351 Water bridges: C:Y.229, C:Y.229 Salt bridges: C:H.277 pi-Stacking: C:F.231, C:F.231 AMP.11: 17 residues within 4Å: Chain D: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.10 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.228, D:F.231, D:S.279, D:W.281, D:R.351 Water bridges: D:Y.229, D:Y.229 Salt bridges: D:H.277 pi-Stacking: D:F.231, D:F.231 AMP.14: 17 residues within 4Å: Chain E: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.13 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.228, E:F.231, E:S.279, E:W.281, E:R.351 Water bridges: E:Y.229, E:Y.229 Salt bridges: E:H.277 pi-Stacking: E:F.231, E:F.231 AMP.17: 17 residues within 4Å: Chain F: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.16 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:N.228, F:F.231, F:S.279, F:W.281, F:R.351 Water bridges: F:Y.229, F:Y.229 Salt bridges: F:H.277 pi-Stacking: F:F.231, F:F.231 AMP.20: 17 residues within 4Å: Chain G: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.19 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:E.132, G:N.228, G:F.231, G:S.279, G:W.281, G:R.351 Water bridges: G:Y.229, G:Y.229 Salt bridges: G:H.277 pi-Stacking: G:F.231, G:F.231 AMP.23: 17 residues within 4Å: Chain H: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.22 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:E.132, H:N.228, H:F.231, H:S.279, H:W.281, H:R.351 Water bridges: H:Y.229, H:Y.229 Salt bridges: H:H.277 pi-Stacking: H:F.231, H:F.231 AMP.26: 17 residues within 4Å: Chain I: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.25 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:E.132, I:N.228, I:F.231, I:S.279, I:W.281, I:R.351 Water bridges: I:Y.229, I:Y.229 Salt bridges: I:H.277 pi-Stacking: I:F.231, I:F.231 AMP.29: 17 residues within 4Å: Chain J: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.28 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:N.228, J:F.231, J:S.279, J:W.281, J:R.351 Water bridges: J:Y.229, J:Y.229 Salt bridges: J:H.277 pi-Stacking: J:F.231, J:F.231 AMP.32: 17 residues within 4Å: Chain K: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.31 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:N.228, K:F.231, K:S.279, K:W.281, K:R.351 Water bridges: K:Y.229, K:Y.229 Salt bridges: K:H.277 pi-Stacking: K:F.231, K:F.231 AMP.35: 17 residues within 4Å: Chain L: Y.128, F.129, G.130, E.132, G.215, H.216, N.228, Y.229, Q.230, F.231, H.277, S.279, W.281, R.351, K.360, R.363 Ligands: MN.34 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:N.228, L:F.231, L:S.279, L:W.281, L:R.351 Water bridges: L:Y.229, L:Y.229 Salt bridges: L:H.277 pi-Stacking: L:F.231, L:F.231

12 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 11 residues within 4Å: Chain A: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.134, A:N.270, A:G.271, A:G.273, A:R.328, A:R.367 Water bridges: A:E.334 Salt bridges: A:K.264, A:H.275, A:H.275, A:R.328 CIT.6: 11 residues within 4Å: Chain B: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:E.134, B:N.270, B:G.271, B:G.273, B:R.328, B:R.367 Water bridges: B:E.334 Salt bridges: B:K.264, B:H.275, B:H.275, B:R.328 CIT.9: 11 residues within 4Å: Chain C: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.134, C:N.270, C:G.271, C:G.273, C:R.328, C:R.367 Water bridges: C:E.334 Salt bridges: C:K.264, C:H.275, C:H.275, C:R.328 CIT.12: 11 residues within 4Å: Chain D: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:E.134, D:N.270, D:G.271, D:G.273, D:R.328, D:R.367 Water bridges: D:E.334 Salt bridges: D:K.264, D:H.275, D:H.275, D:R.328 CIT.15: 11 residues within 4Å: Chain E: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:E.134, E:N.270, E:G.271, E:G.273, E:R.328, E:R.367 Water bridges: E:E.334 Salt bridges: E:K.264, E:H.275, E:H.275, E:R.328 CIT.18: 11 residues within 4Å: Chain F: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:E.134, F:N.270, F:G.271, F:G.273, F:R.328, F:R.367 Water bridges: F:E.334 Salt bridges: F:K.264, F:H.275, F:H.275, F:R.328 CIT.21: 11 residues within 4Å: Chain G: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:E.134, G:N.270, G:G.271, G:G.273, G:R.328, G:R.367 Water bridges: G:E.334 Salt bridges: G:K.264, G:H.275, G:H.275, G:R.328 CIT.24: 11 residues within 4Å: Chain H: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:E.134, H:N.270, H:G.271, H:G.273, H:R.328, H:R.367 Water bridges: H:E.334 Salt bridges: H:K.264, H:H.275, H:H.275, H:R.328 CIT.27: 11 residues within 4Å: Chain I: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:E.134, I:N.270, I:G.271, I:G.273, I:R.328, I:R.367 Water bridges: I:E.334 Salt bridges: I:K.264, I:H.275, I:H.275, I:R.328 CIT.30: 11 residues within 4Å: Chain J: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:E.134, J:N.270, J:G.271, J:G.273, J:R.328, J:R.367 Water bridges: J:E.334 Salt bridges: J:K.264, J:H.275, J:H.275, J:R.328 CIT.33: 11 residues within 4Å: Chain K: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:E.134, K:N.270, K:G.271, K:G.273, K:R.328, K:R.367 Water bridges: K:E.334 Salt bridges: K:K.264, K:H.275, K:H.275, K:R.328 CIT.36: 11 residues within 4Å: Chain L: E.134, N.270, G.271, G.273, H.275, R.328, Y.333, E.334, A.335, P.336, R.367 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:E.134, L:N.270, L:G.271, L:G.273, L:R.328, L:R.367 Water bridges: L:E.334 Salt bridges: L:K.264, L:H.275, L:H.275, L:R.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gill, H.S. et al., Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation. Biochemistry (2002)

Release Date

2002-07-24

Peptides

glutamine synthetase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
O

D
P

E
Q

F
R

G
S

H
T

I
U

J
V

K
W

L
X

glutamine synthetase

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