SMTL ID : 2cz8.1 (1 other biounit)

Crystal Structure of tt0972 protein from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-12-mer

Ligands

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: K.6, V.8 Chain B: K.6, V.8 Chain C: K.6, V.8 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 1 interactions with chain B Water bridges: C:K.6, C:K.6, A:K.6, A:K.6 Salt bridges: C:K.6, A:K.6, B:K.6 PO4.4: 6 residues within 4Å: Chain B: T.13, S.14, E.15, E.55 Chain C: G.2, K.3 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:T.13, B:T.13, B:E.15, B:E.15, C:K.3 Water bridges: B:E.15, B:E.15, B:E.15, B:E.15, B:E.55, C:K.3, C:K.3 Salt bridges: C:K.3 PO4.8: 5 residues within 4Å: Chain D: K.6 Chain H: K.6 Chain L: K.6 Ligands: PO4.18, PO4.28 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H, 1 interactions with chain L Salt bridges: D:K.6, H:K.6, L:K.6 PO4.9: 6 residues within 4Å: Chain D: T.13, S.14, E.15, E.55 Chain L: G.2, K.3 9 PLIP interactions: 4 interactions with chain L, 5 interactions with chain D Hydrogen bonds: L:K.3, D:T.13, D:T.13 Water bridges: L:K.3, L:K.3, D:E.15, D:E.15, D:E.15 Salt bridges: L:K.3 PO4.11: 6 residues within 4Å: Chain E: K.6, V.8 Chain F: K.6, V.8 Chain G: K.6, V.8 7 PLIP interactions: 3 interactions with chain G, 3 interactions with chain E, 1 interactions with chain F Water bridges: G:K.6, G:K.6, E:K.6, E:K.6 Salt bridges: G:K.6, E:K.6, F:K.6 PO4.14: 6 residues within 4Å: Chain F: T.13, S.14, E.15, E.55 Chain G: G.2, K.3 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:T.13, F:T.13, F:E.15, F:E.15, G:K.3 Water bridges: F:E.15, F:E.15, F:E.15, F:E.15, F:E.55, G:K.3, G:K.3 Salt bridges: G:K.3 PO4.18: 5 residues within 4Å: Chain D: K.6 Chain H: K.6 Chain L: K.6 Ligands: PO4.8, PO4.28 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D, 1 interactions with chain H Salt bridges: L:K.6, D:K.6, H:K.6 PO4.19: 6 residues within 4Å: Chain D: G.2, K.3 Chain H: T.13, S.14, E.15, E.55 9 PLIP interactions: 5 interactions with chain H, 4 interactions with chain D Hydrogen bonds: H:T.13, H:T.13, D:K.3 Water bridges: H:E.15, H:E.15, H:E.15, D:K.3, D:K.3 Salt bridges: D:K.3 PO4.21: 6 residues within 4Å: Chain I: K.6, V.8 Chain J: K.6, V.8 Chain K: K.6, V.8 7 PLIP interactions: 3 interactions with chain K, 3 interactions with chain I, 1 interactions with chain J Water bridges: K:K.6, K:K.6, I:K.6, I:K.6 Salt bridges: K:K.6, I:K.6, J:K.6 PO4.24: 6 residues within 4Å: Chain J: T.13, S.14, E.15, E.55 Chain K: G.2, K.3 13 PLIP interactions: 9 interactions with chain J, 4 interactions with chain K Hydrogen bonds: J:T.13, J:T.13, J:E.15, J:E.15, K:K.3 Water bridges: J:E.15, J:E.15, J:E.15, J:E.15, J:E.55, K:K.3, K:K.3 Salt bridges: K:K.3 PO4.28: 5 residues within 4Å: Chain D: K.6 Chain H: K.6 Chain L: K.6 Ligands: PO4.8, PO4.18 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D, 1 interactions with chain H Salt bridges: L:K.6, D:K.6, H:K.6 PO4.29: 6 residues within 4Å: Chain H: G.2, K.3 Chain L: T.13, S.14, E.15, E.55 9 PLIP interactions: 4 interactions with chain H, 5 interactions with chain L Hydrogen bonds: H:K.3, L:T.13, L:T.13 Water bridges: H:K.3, H:K.3, L:E.15, L:E.15, L:E.15 Salt bridges: H:K.3

6 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: E.19 Chain E: E.19 Chain I: E.19 Ligands: K.12, K.22 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 1 interactions with chain E Metal complexes: I:E.19, A:E.19, E:E.19 K.6: 3 residues within 4Å: Chain C: E.19 Chain D: E.19 Chain F: E.19 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain F Metal complexes: D:E.19, C:E.19, F:E.19 K.12: 5 residues within 4Å: Chain A: E.19 Chain E: E.19 Chain I: E.19 Ligands: K.2, K.22 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 1 interactions with chain E Metal complexes: I:E.19, A:E.19, E:E.19 K.16: 3 residues within 4Å: Chain G: E.19 Chain H: E.19 Chain J: E.19 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain G, 1 interactions with chain H Metal complexes: J:E.19, G:E.19, H:E.19 K.22: 5 residues within 4Å: Chain A: E.19 Chain E: E.19 Chain I: E.19 Ligands: K.2, K.12 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain I, 1 interactions with chain A Metal complexes: E:E.19, I:E.19, A:E.19 K.26: 3 residues within 4Å: Chain B: E.19 Chain K: E.19 Chain L: E.19 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain K, 1 interactions with chain L Metal complexes: B:E.19, K:E.19, L:E.19

12 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.3: 17 residues within 4Å: Chain A: K.3, Y.5, L.33, R.34, H.35, L.36, D.37, W.38, R.65 Chain C: V.11, R.45, Q.57, V.59 Chain E: R.45, T.47, Q.57 Ligands: FAD.15 21 PLIP interactions: 3 interactions with chain E, 16 interactions with chain A, 2 interactions with chain C Hydrogen bonds: E:R.45, E:Q.57, E:Q.57, A:L.33, A:H.35, A:H.35, A:L.36 Hydrophobic interactions: A:W.38, C:V.59 Water bridges: A:R.30, A:D.37, A:D.37, A:D.37, A:D.37, A:D.37, C:Q.57 Salt bridges: A:K.3, A:R.65 pi-Stacking: A:W.38, A:W.38, A:W.38 FAD.5: 15 residues within 4Å: Chain A: V.11, Q.57, V.59 Chain B: K.3, Y.5, R.30, R.34, H.35, D.37, W.38, R.65 Chain K: R.45, T.47, Q.57 Ligands: FAD.23 19 PLIP interactions: 3 interactions with chain K, 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: K:R.45, K:Q.57, K:Q.57, B:Y.5, B:R.30, B:H.35 Hydrophobic interactions: B:Y.5, B:W.38, A:V.59 Water bridges: B:L.36, B:D.37, B:D.37, B:D.37 Salt bridges: B:K.3, B:R.65, B:R.65 pi-Stacking: B:W.38, B:W.38, B:W.38 FAD.7: 14 residues within 4Å: Chain B: V.11, R.45, Q.57, V.59 Chain C: K.3, Y.5, H.35, D.37, W.38, R.65 Chain D: R.45, T.47, Q.57 Ligands: FAD.30 15 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: C:W.38, B:V.59 Hydrogen bonds: C:H.35, D:R.45, D:Q.57, D:Q.57 Water bridges: C:R.30, C:R.30, C:D.37, C:D.37, B:Q.57 Salt bridges: C:R.65 pi-Stacking: C:W.38, C:W.38, C:W.38 FAD.10: 20 residues within 4Å: Chain D: K.3, Y.5, L.33, R.34, H.35, L.36, D.37, W.38, R.65 Chain F: R.45, T.47, I.48, G.49, E.50, Q.57 Chain H: V.11, R.45, Q.57, V.59 Ligands: FAD.17 20 PLIP interactions: 15 interactions with chain D, 4 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: D:W.38, H:V.59 Hydrogen bonds: D:Y.5, D:R.34, D:H.35, D:H.35, D:L.36, D:D.37, D:R.65, F:R.45, F:E.50, F:Q.57, F:Q.57 Water bridges: D:D.37 Salt bridges: D:H.35, D:R.65 pi-Stacking: D:H.35, D:W.38, D:W.38, D:W.38 FAD.13: 17 residues within 4Å: Chain E: K.3, Y.5, L.33, R.34, H.35, L.36, D.37, W.38, R.65 Chain G: V.11, R.45, Q.57, V.59 Chain I: R.45, T.47, Q.57 Ligands: FAD.25 21 PLIP interactions: 16 interactions with chain E, 3 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: E:W.38, G:V.59 Hydrogen bonds: E:L.33, E:H.35, E:H.35, E:L.36, I:R.45, I:Q.57, I:Q.57 Water bridges: E:R.30, E:D.37, E:D.37, E:D.37, E:D.37, E:D.37, G:Q.57 Salt bridges: E:K.3, E:R.65 pi-Stacking: E:W.38, E:W.38, E:W.38 FAD.15: 15 residues within 4Å: Chain C: R.45, T.47, Q.57 Chain E: V.11, Q.57, V.59 Chain F: K.3, Y.5, R.30, R.34, H.35, D.37, W.38, R.65 Ligands: FAD.3 19 PLIP interactions: 15 interactions with chain F, 3 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: F:Y.5, F:W.38, E:V.59 Hydrogen bonds: F:Y.5, F:R.30, F:H.35, C:R.45, C:Q.57, C:Q.57 Water bridges: F:L.36, F:D.37, F:D.37, F:D.37 Salt bridges: F:K.3, F:R.65, F:R.65 pi-Stacking: F:W.38, F:W.38, F:W.38 FAD.17: 14 residues within 4Å: Chain F: V.11, R.45, Q.57, V.59 Chain G: K.3, Y.5, H.35, D.37, W.38, R.65 Chain H: R.45, T.47, Q.57 Ligands: FAD.10 15 PLIP interactions: 3 interactions with chain H, 10 interactions with chain G, 2 interactions with chain F Hydrogen bonds: H:R.45, H:Q.57, H:Q.57, G:H.35 Hydrophobic interactions: G:W.38, F:V.59 Water bridges: G:R.30, G:R.30, G:D.37, G:D.37, F:Q.57 Salt bridges: G:R.65 pi-Stacking: G:W.38, G:W.38, G:W.38 FAD.20: 20 residues within 4Å: Chain H: K.3, Y.5, L.33, R.34, H.35, L.36, D.37, W.38, R.65 Chain J: R.45, T.47, I.48, G.49, E.50, Q.57 Chain L: V.11, R.45, Q.57, V.59 Ligands: FAD.27 20 PLIP interactions: 15 interactions with chain H, 4 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: H:W.38, L:V.59 Hydrogen bonds: H:Y.5, H:R.34, H:H.35, H:H.35, H:L.36, H:D.37, H:R.65, J:R.45, J:E.50, J:Q.57, J:Q.57 Water bridges: H:D.37 Salt bridges: H:H.35, H:R.65 pi-Stacking: H:H.35, H:W.38, H:W.38, H:W.38 FAD.23: 17 residues within 4Å: Chain A: R.45, T.47, Q.57 Chain I: K.3, Y.5, L.33, R.34, H.35, L.36, D.37, W.38, R.65 Chain K: V.11, R.45, Q.57, V.59 Ligands: FAD.5 21 PLIP interactions: 3 interactions with chain A, 16 interactions with chain I, 2 interactions with chain K Hydrogen bonds: A:R.45, A:Q.57, A:Q.57, I:L.33, I:H.35, I:H.35, I:L.36 Hydrophobic interactions: I:W.38, K:V.59 Water bridges: I:R.30, I:D.37, I:D.37, I:D.37, I:D.37, I:D.37, K:Q.57 Salt bridges: I:K.3, I:R.65 pi-Stacking: I:W.38, I:W.38, I:W.38 FAD.25: 15 residues within 4Å: Chain G: R.45, T.47, Q.57 Chain I: V.11, Q.57, V.59 Chain J: K.3, Y.5, R.30, R.34, H.35, D.37, W.38, R.65 Ligands: FAD.13 19 PLIP interactions: 15 interactions with chain J, 3 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: J:Y.5, J:W.38, I:V.59 Hydrogen bonds: J:Y.5, J:R.30, J:H.35, G:R.45, G:Q.57, G:Q.57 Water bridges: J:L.36, J:D.37, J:D.37, J:D.37 Salt bridges: J:K.3, J:R.65, J:R.65 pi-Stacking: J:W.38, J:W.38, J:W.38 FAD.27: 14 residues within 4Å: Chain J: V.11, R.45, Q.57, V.59 Chain K: K.3, Y.5, H.35, D.37, W.38, R.65 Chain L: R.45, T.47, Q.57 Ligands: FAD.20 15 PLIP interactions: 2 interactions with chain J, 3 interactions with chain L, 10 interactions with chain K Hydrophobic interactions: J:V.59, K:W.38 Water bridges: J:Q.57, K:R.30, K:R.30, K:D.37, K:D.37 Hydrogen bonds: L:R.45, L:Q.57, L:Q.57, K:H.35 Salt bridges: K:R.65 pi-Stacking: K:W.38, K:W.38, K:W.38 FAD.30: 20 residues within 4Å: Chain B: R.45, T.47, I.48, G.49, E.50, Q.57 Chain D: V.11, R.45, Q.57, V.59 Chain L: K.3, Y.5, L.33, R.34, H.35, L.36, D.37, W.38, R.65 Ligands: FAD.7 20 PLIP interactions: 15 interactions with chain L, 1 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: L:W.38, D:V.59 Hydrogen bonds: L:Y.5, L:R.34, L:H.35, L:H.35, L:L.36, L:D.37, L:R.65, B:R.45, B:E.50, B:Q.57, B:Q.57 Water bridges: L:D.37 Salt bridges: L:H.35, L:R.65 pi-Stacking: L:H.35, L:W.38, L:W.38, L:W.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumei, M. et al., Crystal Structure of tt0972 protein from Thermus thermophilus. To be Published

Release Date

2006-09-19

Peptides

tt0972 protein: 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

tt0972 protein

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