SMTL ID : 1zfn.3 (3 other biounits)

Structural Analysis of Escherichia coli ThiF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.171, C.174, C.242, C.245 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.171, A:C.174, A:C.242 ZN.3: 6 residues within 4Å: Chain B: C.171, R.173, C.174, C.242, V.244, C.245 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.171, B:C.174, B:C.242, B:C.245 ZN.5: 4 residues within 4Å: Chain C: C.171, C.174, C.242, C.245 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.171, C:C.174, C:C.242, C:C.245 ZN.7: 4 residues within 4Å: Chain D: C.171, C.174, C.242, C.245 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.171, D:C.174, D:C.242, D:C.245 ZN.9: 4 residues within 4Å: Chain E: C.171, C.174, C.242, C.245 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.171, E:C.174, E:C.242 ZN.11: 6 residues within 4Å: Chain F: C.171, R.173, C.174, C.242, V.244, C.245 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.171, F:C.174, F:C.242, F:C.245 ZN.13: 4 residues within 4Å: Chain G: C.171, C.174, C.242, C.245 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.171, G:C.174, G:C.242, G:C.245 ZN.15: 4 residues within 4Å: Chain H: C.171, C.174, C.242, C.245 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.171, H:C.174, H:C.242, H:C.245 ZN.17: 4 residues within 4Å: Chain I: C.171, C.174, C.242, C.245 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.171, I:C.174, I:C.242 ZN.19: 6 residues within 4Å: Chain J: C.171, R.173, C.174, C.242, V.244, C.245 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.171, J:C.174, J:C.242, J:C.245 ZN.21: 4 residues within 4Å: Chain K: C.171, C.174, C.242, C.245 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.171, K:C.174, K:C.242, K:C.245 ZN.23: 4 residues within 4Å: Chain L: C.171, C.174, C.242, C.245 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.171, L:C.174, L:C.242, L:C.245

12 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 residues within 4Å: Chain A: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 Chain B: R.13 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.38, A:G.40, A:D.63, A:D.63, A:S.68, A:Q.73, A:K.85, A:L.109, A:L.109, A:T.133 Salt bridges: A:R.72, A:R.72, A:R.72, A:K.85, B:R.13 ATP.4: 21 residues within 4Å: Chain A: R.13 Chain B: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.38, B:L.38, B:G.40, B:D.61, B:D.63, B:D.63, B:S.68, B:Q.73, B:L.109, B:L.109, B:T.133 Salt bridges: B:R.72, B:R.72, B:R.72, B:K.85, A:R.13 ATP.6: 20 residues within 4Å: Chain C: I.36, G.37, L.38, G.39, G.40, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 Chain D: R.13 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:L.38, C:L.38, C:G.40, C:S.68, C:Q.73, C:R.108, C:L.109, C:L.109, C:D.129 Salt bridges: C:R.72, C:R.72, C:K.85, D:R.13 ATP.8: 21 residues within 4Å: Chain C: R.13 Chain D: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:L.38, D:G.40, D:D.63, D:S.68, D:Q.73, D:K.85, D:L.109, D:L.109, D:D.129, D:N.130 Salt bridges: D:R.72, D:R.72, D:R.72, D:K.85, D:K.85, C:R.13 ATP.10: 21 residues within 4Å: Chain E: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 Chain F: R.13 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:L.38, E:G.40, E:D.63, E:D.63, E:S.68, E:Q.73, E:K.85, E:L.109, E:L.109, E:D.129 Salt bridges: E:R.72, E:R.72, E:R.72, E:K.85, F:R.13 ATP.12: 21 residues within 4Å: Chain E: R.13 Chain F: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:L.38, F:L.38, F:G.40, F:D.61, F:D.63, F:D.63, F:S.68, F:Q.73, F:L.109, F:L.109, F:T.133 Salt bridges: F:R.72, F:R.72, F:R.72, F:K.85, E:R.13 ATP.14: 20 residues within 4Å: Chain G: I.36, G.37, L.38, G.39, G.40, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 Chain H: R.13 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:L.38, G:L.38, G:G.40, G:S.68, G:Q.73, G:R.108, G:L.109, G:L.109, G:T.133 Salt bridges: G:R.72, G:R.72, G:K.85, H:R.13 ATP.16: 21 residues within 4Å: Chain G: R.13 Chain H: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 16 PLIP interactions: 15 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:L.38, H:G.40, H:D.63, H:S.68, H:Q.73, H:K.85, H:L.109, H:L.109, H:N.130, H:T.133 Salt bridges: H:R.72, H:R.72, H:R.72, H:K.85, H:K.85, G:R.13 ATP.18: 21 residues within 4Å: Chain I: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 Chain J: R.13 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:L.38, I:G.40, I:D.63, I:S.68, I:Q.73, I:K.85, I:L.109, I:L.109, I:D.129 Salt bridges: I:R.72, I:R.72, I:R.72, I:K.85, J:R.13 ATP.20: 21 residues within 4Å: Chain I: R.13 Chain J: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 15 PLIP interactions: 14 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:L.38, J:L.38, J:G.40, J:D.61, J:D.63, J:S.68, J:Q.73, J:L.109, J:L.109, J:D.129 Salt bridges: J:R.72, J:R.72, J:R.72, J:K.85, I:R.13 ATP.22: 20 residues within 4Å: Chain K: I.36, G.37, L.38, G.39, G.40, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 Chain L: R.13 13 PLIP interactions: 12 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:L.38, K:L.38, K:G.40, K:S.68, K:Q.73, K:R.108, K:L.109, K:L.109, K:T.133 Salt bridges: K:R.72, K:R.72, K:K.85, L:R.13 ATP.24: 21 residues within 4Å: Chain K: R.13 Chain L: I.36, G.37, L.38, G.39, G.40, A.60, D.61, D.63, S.68, N.69, R.72, Q.73, K.85, Q.107, R.108, L.109, C.127, T.128, D.129, T.133 16 PLIP interactions: 15 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:L.38, L:G.40, L:D.63, L:S.68, L:Q.73, L:K.85, L:L.109, L:L.109, L:D.129, L:N.130 Salt bridges: L:R.72, L:R.72, L:R.72, L:K.85, L:K.85, K:R.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duda, D.M. et al., Structural Analysis of Escherichia Coli ThiF. J.Mol.Biol. (2005)

Release Date

2005-06-14

Peptides

Adenylyltransferase thiF: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Adenylyltransferase thiF

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