SMTL ID : 4ki8.1

Crystal structure of a GroEL-ADP complex in the relaxed allosteric state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-heptamer

Ligands

7 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 21 residues within 4Å: Chain A: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.2, K.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.32, A:D.87, A:G.88, A:G.88, A:T.90, A:T.91, A:T.91, A:G.415, A:N.479, A:A.480, A:A.481, A:D.495 Water bridges: A:G.53, A:G.53, A:T.90, A:T.91, A:T.91 ADP.12: 21 residues within 4Å: Chain B: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.13, K.14 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.32, B:D.87, B:D.87, B:G.88, B:T.90, B:T.90, B:T.91, B:G.415, B:N.479, B:A.480, B:A.481, B:D.495 Water bridges: B:D.87, B:D.87, B:D.87, B:D.87, B:T.91, B:T.91, B:T.91, B:N.153, B:N.153 ADP.21: 21 residues within 4Å: Chain C: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.22, K.23 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:G.32, C:D.87, C:D.87, C:G.88, C:T.90, C:T.91, C:G.415, C:N.479, C:A.480, C:A.481, C:D.495 Water bridges: C:T.89, C:T.90, C:T.90, C:T.91, C:T.91, C:T.91, C:T.91, C:N.153, C:D.495 ADP.25: 20 residues within 4Å: Chain D: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.26, K.27 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:G.32, D:D.87, D:D.87, D:G.88, D:T.90, D:T.91, D:G.415, D:N.479, D:A.480, D:A.481, D:D.495 Water bridges: D:G.53, D:G.53, D:D.87, D:D.87, D:D.87, D:T.89, D:T.90, D:T.90, D:T.91, D:T.91, D:T.91, D:T.91, D:N.153, D:G.416, D:D.495 ADP.32: 20 residues within 4Å: Chain E: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.33, K.34 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:G.32, E:G.88, E:G.88, E:T.90, E:T.91, E:G.415, E:G.416, E:N.479, E:A.480, E:A.481, E:D.495 Water bridges: E:D.87, E:T.89, E:T.89, E:T.90, E:T.90, E:T.91, E:T.91, E:T.91, E:N.153 ADP.39: 23 residues within 4Å: Chain F: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, N.153, S.154, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.40, K.41 22 PLIP interactions: 22 interactions with chain F Hydrogen bonds: F:G.32, F:D.87, F:D.87, F:G.88, F:T.90, F:T.90, F:T.91, F:T.91, F:N.153, F:G.415, F:N.479, F:A.480, F:A.481, F:D.495 Water bridges: F:G.35, F:G.53, F:G.53, F:T.89, F:T.91, F:N.153, F:N.153, F:D.495 ADP.45: 19 residues within 4Å: Chain G: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, G.414, G.415, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.46, K.47 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:G.32, G:D.87, G:D.87, G:G.88, G:T.90, G:T.91, G:T.91, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495 Water bridges: G:T.89, G:T.90, G:T.90, G:T.91, G:D.495

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.87 Ligands: ADP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.87, A:D.87, H2O.1, H2O.1, H2O.2 MG.13: 2 residues within 4Å: Chain B: D.87 Ligands: ADP.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.87, B:D.87, H2O.6, H2O.6, H2O.6 MG.22: 2 residues within 4Å: Chain C: D.87 Ligands: ADP.21 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.87, C:D.87, H2O.10, H2O.10, H2O.11 MG.26: 2 residues within 4Å: Chain D: D.87 Ligands: ADP.25 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.87, D:D.87, H2O.12, H2O.13, H2O.14 MG.33: 2 residues within 4Å: Chain E: D.87 Ligands: ADP.32 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.87, E:D.87, H2O.16, H2O.17, H2O.17 MG.40: 3 residues within 4Å: Chain F: D.87, N.153 Ligands: ADP.39 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.87, F:D.87, H2O.18, H2O.18, H2O.18 MG.46: 2 residues within 4Å: Chain G: D.87 Ligands: ADP.45 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.87, G:D.87, H2O.20, H2O.21, H2O.21

9 x K: POTASSIUM ION(Non-covalent)

K.3: 3 residues within 4Å: Chain A: T.30, K.51 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.30, H2O.1, H2O.2, H2O.3, H2O.3 K.14: 3 residues within 4Å: Chain B: T.30, K.51 Ligands: ADP.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.30, B:K.51, H2O.7, H2O.7 K.23: 4 residues within 4Å: Chain C: T.30, G.32, K.51 Ligands: ADP.21 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.30, H2O.9, H2O.11 K.27: 4 residues within 4Å: Chain D: T.30, K.51, N.153 Ligands: ADP.25 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.30, D:K.51, H2O.14, H2O.14, H2O.14 K.34: 3 residues within 4Å: Chain E: T.30, G.32 Ligands: ADP.32 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.30, H2O.16, H2O.16 K.41: 3 residues within 4Å: Chain F: T.30, K.51 Ligands: ADP.39 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.30, F:K.51, H2O.19, H2O.19, H2O.19 K.43: 2 residues within 4Å: Chain F: E.460, E.483 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.483, H2O.20 K.47: 3 residues within 4Å: Chain G: T.30, K.51 Ligands: ADP.45 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:T.30, G:K.51, H2O.23, H2O.23, H2O.23 K.52: 4 residues within 4Å: Chain A: D.115, N.433 Chain G: E.460, E.483 No protein-ligand interaction detected (PLIP)

19 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 5 residues within 4Å: Chain A: V.189, V.190, E.191, Q.343, A.373 Ligand excluded by PLIP MPD.5: 5 residues within 4Å: Chain A: N.10, V.14, L.17, L.104, A.108 Ligand excluded by PLIP MPD.6: 4 residues within 4Å: Chain A: E.518 Chain G: R.36, L.456, N.457 Ligand excluded by PLIP MPD.7: 3 residues within 4Å: Chain A: Q.505, Y.506, S.509 Ligand excluded by PLIP MPD.8: 5 residues within 4Å: Chain A: R.36, Q.453, L.456, N.457 Chain B: E.518 Ligand excluded by PLIP MPD.9: 9 residues within 4Å: Chain A: A.83, A.84, A.85, G.86, H.401, R.404, A.405, E.408, K.498 Ligand excluded by PLIP MPD.15: 5 residues within 4Å: Chain B: N.10, V.14, L.104, K.105, A.108 Ligand excluded by PLIP MPD.16: 6 residues within 4Å: Chain B: V.29, R.36, Q.453, L.456, N.457 Chain C: E.518 Ligand excluded by PLIP MPD.17: 3 residues within 4Å: Chain B: R.501, Q.505, Y.506 Ligand excluded by PLIP MPD.18: 3 residues within 4Å: Chain B: E.102, V.438, R.445 Ligand excluded by PLIP MPD.19: 7 residues within 4Å: Chain B: N.82, A.83, A.84, G.86, H.401, E.408, K.498 Ligand excluded by PLIP MPD.24: 5 residues within 4Å: Chain C: V.14, L.17, L.104, K.105, A.108 Ligand excluded by PLIP MPD.28: 6 residues within 4Å: Chain D: N.10, V.14, L.17, L.104, K.105, A.108 Ligand excluded by PLIP MPD.29: 3 residues within 4Å: Chain D: I.175, T.176, V.324 Ligand excluded by PLIP MPD.30: 3 residues within 4Å: Chain D: R.18, V.22, D.25 Ligand excluded by PLIP MPD.35: 3 residues within 4Å: Chain E: E.102, V.438, R.445 Ligand excluded by PLIP MPD.42: 4 residues within 4Å: Chain F: I.175, T.176, V.324, T.331 Ligand excluded by PLIP MPD.48: 5 residues within 4Å: Chain G: V.14, L.17, L.104, K.105, A.108 Ligand excluded by PLIP MPD.49: 2 residues within 4Å: Chain G: Q.505, Y.506 Ligand excluded by PLIP

11 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: D.41, K.42, S.43 Chain B: N.68 No protein-ligand interaction detected (PLIP) CA.11: 1 residues within 4Å: Chain A: R.445 No protein-ligand interaction detected (PLIP) CA.20: 2 residues within 4Å: Chain B: E.460 Chain C: N.112 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.460, H2O.7, H2O.7, H2O.11 CA.31: 1 residues within 4Å: Chain D: N.68 No protein-ligand interaction detected (PLIP) CA.36: 2 residues within 4Å: Chain D: S.43 Chain E: K.65 No protein-ligand interaction detected (PLIP) CA.37: 1 residues within 4Å: Chain E: S.43 No protein-ligand interaction detected (PLIP) CA.38: 1 residues within 4Å: Chain E: E.130 No protein-ligand interaction detected (PLIP) CA.44: 1 residues within 4Å: Chain F: S.43 No protein-ligand interaction detected (PLIP) CA.50: 1 residues within 4Å: Chain G: S.43 No protein-ligand interaction detected (PLIP) CA.51: 1 residues within 4Å: Chain G: R.445 No protein-ligand interaction detected (PLIP) CA.53: 2 residues within 4Å: Chain A: P.113 Chain G: R.36 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fei, X. et al., Crystal structure of a GroEL-ADP complex in the relaxed allosteric state at 2.7 A resolution. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-07-17

Peptides

GroEL protein: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

GroEL protein

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