Research workbench
NH3-bound rt xfel structure of photosystem II 500 ms after the 2ND illumination (2F) at 2.8 a resolution
Analyse NH3-bound rt xfel structure of photosystem II 500 ms after the 2ND illumination… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KAI
- Type
- protein
- Length
- 5,316 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DIQ0, Q9F1L5, P0A386, Q8DJI1, Q9F1R6, Q8DHJ2, Q8DKM3
- Ligands
- CLA, UNL, BCR, LMG, LHG, SQD, DGD, PHO, PL9, OEX, BCT, HEM, HEC, FE2, CL
Structure
x-ray diffraction · 22 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | — | protein | 334 | — | P0A444 |
| B, b | — | protein | 504 | — | Q8DIQ1 |
| C, c | — | protein | 451 | — | Q8DIF8 |
| D, d | — | protein | 341 | — | Q8CM25 |
| E | — | protein | 81 | — | Q8DIP0 |
| F, f | — | protein | 34 | — | Q8DIN9 |
| H, h | — | protein | 63 | — | Q8DJ43 |
| I, i | — | protein | 36 | — | Q8DJZ6 |
| J, j | — | protein | 36 | — | P59087 |
| K, k | — | protein | 37 | — | Q9F1K9 |
| L, l | — | protein | 37 | — | Q8DIN8 |
| M, m | — | protein | 33 | — | Q8DHA7 |
| O, o | — | protein | 244 | — | P0A431 |
| T, t | — | protein | 30 | — | Q8DIQ0 |
| U, u | — | protein | 97 | — | Q9F1L5 |
| V, v | — | protein | 137 | — | P0A386 |
| Y | — | protein | 27 | — | Q8DJI1 |
| X, x | — | protein | 38 | — | Q9F1R6 |
| Z, z | — | protein | 62 | — | Q8DHJ2 |
| R, r | — | protein | 34 | — | Q8DKM3 |
| e | — | protein | 82 | — | Q8DIP0 |
| y | — | protein | 30 | — | Q8DJI1 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, I, B, H, L, M, t, C, K, Y, Z, X, a, d, i, b, h, l, m, c, k, y, z, x
- UNL · Unknown ligand · ligand · 23 copies · chains A, B, D, a, H, I, M, b, h, T, m, d, x, i, j, t, c, z
- BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, K, Z, D, F, J, H, X, Y, a, i, T, b, m, c, k, z, d, f, j, h, y
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 16 copies · chains A, T, b, B, C, I, K, Y, D, F, J, L, M, a, t, c, i, l, m, k, y, d, f, j
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, B, D, M, L, T, C, E, a, c, d, b, l, m, t, e
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 9 copies · chains A, C, D, K, O, b, B, H, L, l, m, t, E, F, X, R, I, a, c, d, k, M, T, e, f, x, r
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains A, C, J, V, B, D, H, a, c, j, d, v, b, h
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 4 copies · chains A, D, F, X, L, T, a, d, f, x, l, t
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, R, e, f, r
- HEC · Heme C · ligand · 2 copies · chains V, v
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5KAI · NH3-bound RT XFEL structure of Photosystem II 500 ms after the 2nd illumination (2F) at… · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A444
- Every structure of UniProt Q8DIQ1
- Every structure of UniProt Q8DIF8
- Every structure of UniProt Q8CM25
- Every structure of UniProt Q8DIP0
- Every structure of UniProt Q8DIN9
- Every structure of UniProt Q8DJ43
- Every structure of UniProt Q8DJZ6
- Every structure of UniProt P59087
- Every structure of UniProt Q9F1K9
- Every structure of UniProt Q8DIN8
- Every structure of UniProt Q8DHA7
- Every structure of UniProt P0A431
- Every structure of UniProt Q8DIQ0
- Every structure of UniProt Q9F1L5
- Every structure of UniProt P0A386
- Every structure of UniProt Q8DJI1
- Every structure of UniProt Q9F1R6
- Every structure of UniProt Q8DHJ2
- Every structure of UniProt Q8DKM3
- Elsewhere: RCSB PDB 5KAI · PDBe 5KAI · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt P59087 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt Q8DHA7 · UniProt P0A431 · UniProt Q8DIQ0 · UniProt Q9F1L5 · UniProt P0A386 · UniProt Q8DJI1 · UniProt Q9F1R6 · UniProt Q8DHJ2 · UniProt Q8DKM3
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