SMTL ID : 2i52.3 (3 other biounits)

Crystal structure of protein PTO0218 from Picrophilus torridus, Pfam DUF372

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-12-mer

Ligands

24 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: H.31, T.34 Chain D: T.34 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.34, H2O.4, H2O.8, H2O.12, H2O.13 CA.2: 2 residues within 4Å: Chain B: E.47 Chain F: E.47 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: F:E.47, B:E.47, H2O.5, H2O.6, H2O.21 CA.3: 3 residues within 4Å: Chain B: T.34 Chain C: H.31, T.34 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.34, C:T.34, H2O.2, H2O.5, H2O.12 CA.4: 2 residues within 4Å: Chain B: M.55, I.56 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:M.55, H2O.6, H2O.6, H2O.12 CA.6: 1 residues within 4Å: Chain C: E.47 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.47, H2O.8, H2O.8, H2O.10, H2O.10 CA.7: 1 residues within 4Å: Chain C: N.62 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain D: E.51 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.12, H2O.13, H2O.14, H2O.14, H2O.15 CA.12: 2 residues within 4Å: Chain E: E.47 Ligands: CA.13 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.47, H2O.16, H2O.17, H2O.17, H2O.20 CA.13: 3 residues within 4Å: Chain E: S.66 Ligands: CA.12, CA.15 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:S.66, H2O.16, H2O.17, H2O.17, H2O.17 CA.14: 3 residues within 4Å: Chain K: H.31, T.34 Ligands: CA.31 5 PLIP interactions: 2 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:T.34, K:T.34, H2O.15, H2O.21, H2O.44 CA.15: 2 residues within 4Å: Chain E: S.66 Ligands: CA.13 No protein-ligand interaction detected (PLIP) CA.16: 4 residues within 4Å: Chain F: H.31, T.34 Chain L: T.34 Ligands: CA.33 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.34, F:T.34, H2O.20, H2O.40, H2O.43 CA.18: 3 residues within 4Å: Chain G: H.31, T.34 Chain J: T.34 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:T.34, H2O.27, H2O.31, H2O.34, H2O.36 CA.19: 2 residues within 4Å: Chain H: E.47 Chain L: E.47 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: L:E.47, H:E.47, H2O.28, H2O.29, H2O.44 CA.20: 3 residues within 4Å: Chain H: T.34 Chain I: H.31, T.34 5 PLIP interactions: 2 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:T.34, I:T.34, H2O.25, H2O.28, H2O.35 CA.21: 2 residues within 4Å: Chain H: M.55, I.56 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:M.55, H2O.29, H2O.29, H2O.35 CA.23: 1 residues within 4Å: Chain I: E.47 5 PLIP interactions: 1 interactions with chain I, 4 Ligand-Water interactions Metal complexes: I:E.47, H2O.31, H2O.31, H2O.33, H2O.33 CA.24: 1 residues within 4Å: Chain I: N.62 No protein-ligand interaction detected (PLIP) CA.25: 1 residues within 4Å: Chain J: E.51 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.35, H2O.36, H2O.36, H2O.37, H2O.37 CA.29: 2 residues within 4Å: Chain K: E.47 Ligands: CA.30 5 PLIP interactions: 1 interactions with chain K, 4 Ligand-Water interactions Metal complexes: K:E.47, H2O.39, H2O.40, H2O.40, H2O.43 CA.30: 3 residues within 4Å: Chain K: S.66 Ligands: CA.29, CA.32 5 PLIP interactions: 1 interactions with chain K, 4 Ligand-Water interactions Metal complexes: K:S.66, H2O.39, H2O.40, H2O.40, H2O.40 CA.31: 3 residues within 4Å: Chain E: H.31, T.34 Ligands: CA.14 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.34, E:T.34, H2O.21, H2O.38, H2O.44 CA.32: 2 residues within 4Å: Chain K: S.66 Ligands: CA.30 No protein-ligand interaction detected (PLIP) CA.33: 4 residues within 4Å: Chain F: T.34 Chain L: H.31, T.34 Ligands: CA.16 5 PLIP interactions: 2 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:T.34, L:T.34, H2O.18, H2O.20, H2O.43

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain B: T.13, D.14, I.15, K.98 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain H: T.13, D.14, I.15, K.98 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 10 residues within 4Å: Chain B: P.37, Y.79, S.81 Chain C: F.30, H.31, Y.112, P.113, M.115 Chain D: A.28, Q.57 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:P.113, B:Y.79 Water bridges: D:I.24, D:Q.57, D:Q.57 GOL.10: 8 residues within 4Å: Chain A: Y.79, S.81 Chain C: A.28, Q.57 Chain D: F.30, H.31, Y.112, P.113 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.79, A:S.81 Water bridges: C:I.24, C:Q.57, C:Q.57 GOL.11: 4 residues within 4Å: Chain D: E.90, L.101, V.103, Y.116 No protein-ligand interaction detected (PLIP) GOL.17: 4 residues within 4Å: Chain B: S.44, E.48 Chain F: E.48, E.51 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain B Hydrogen bonds: F:E.51 Water bridges: F:N.62, F:V.63, B:S.44, B:S.44, B:S.44, B:E.48, B:E.48, B:E.48 GOL.26: 10 residues within 4Å: Chain H: P.37, Y.79, S.81 Chain I: F.30, H.31, Y.112, P.113, M.115 Chain J: A.28, Q.57 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I Water bridges: J:I.24, J:Q.57, J:Q.57, I:Y.112 Hydrogen bonds: I:P.113 GOL.27: 8 residues within 4Å: Chain G: Y.79, S.81 Chain I: A.28, Q.57 Chain J: F.30, H.31, Y.112, P.113 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain I Hydrogen bonds: G:S.81 Water bridges: I:I.24, I:Q.57, I:Q.57 GOL.28: 4 residues within 4Å: Chain J: E.90, L.101, V.103, Y.116 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Y.116 GOL.34: 4 residues within 4Å: Chain H: S.44, E.48 Chain L: E.48, E.51 9 PLIP interactions: 5 interactions with chain H, 4 interactions with chain L Water bridges: H:S.44, H:S.44, H:S.44, H:E.48, H:E.48, L:N.62, L:V.63 Hydrogen bonds: L:E.51, L:E.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramagopal, U.A. et al., Structure of hypothetical protein PTO0218 from Picrophilus torridus. To be Published

Release Date

2006-09-12

Peptides

Hypothetical protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

Hypothetical protein

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